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ORCIDJournal of Chemical Information and Modeling, Volume 63
Volume 63, Number 1, January 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
:
Editorial: Machine Learning in Bio-cheminformatics. 1 - Martin Stroet, Stephen Sanderson, Audrey V. Sanzogni, Sharif Nada, Thomas Lee, Bertrand Caron, Alan E. Mark, Paul L. Burn:
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies. 2-8 - Ahmet Yildirim, Mustafa Tekpinar:
Building Quantitative Bridges between Dynamics and Sequences of SARS-CoV-2 Main Protease and a Diverse Set of Thirty-Two Proteins. 9-19 - Rui P. P. Neves, Maria João Ramos, Pedro Alexandrino Fernandes:
Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis. 20-26 - Daniel Vella, Jean-Paul Ebejer:
Few-Shot Learning for Low-Data Drug Discovery. 27-42 - Weimin Zhu, Yi Zhang, Duancheng Zhao, Jianrong Xu, Ling Wang:
HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention. 43-55 - Maria Vittoria Togo, Fabrizio Mastrolorito, Fulvio Ciriaco, Daniela Trisciuzzi, Anna Rita Tondo, Nicola Gambacorta, Loredana Bellantuono, Alfonso Monaco, Francesco Leonetti, Roberto Bellotti, Cosimo Damiano Altomare, Nicola Amoroso, Orazio Nicolotti:
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity. 56-66 - Hao Tian, Xi Jiang, Sian Xiao, Hunter La Force, Eric C. Larson, Peng Tao:
LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories. 67-75 - Ryo Kawada, Katsuhiro Endo, Kenji Yasuoka, Hidekazu Kojima, Nobuyuki Matubayasi:
Prediction of Water Diffusion in Wide Varieties of Polymers with All-Atom Molecular Dynamics Simulations and Deep Generative Models. 76-86 - Omer Kaspi, Osnat Israelsohn-Azulay, Zidon Yigal, Hila Rosengarten, Matea Krmpotic, Sabrina Gouasmia, Iva Bogdanovic-Radovic, Pasi Jalkanen, Anna Liski, Kenichiro Mizohata, Jyrki Räisänen, Zsolt Kasztovszky, Ildikó Harsányi, Raghunath Acharya, Pradeep K. Pujari, Molnár Mihály, Mihaly Braun, Nahum Shabi, Olga Girshevitz, Hanoch Senderowitz:
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments. 87-100 - Jörg Heider, Jonas Kilian, Aleksandra Garifulina, Steffen Hering, Thierry Langer, Thomas Seidel:
Apo2ph4: A Versatile Workflow for the Generation of Receptor-based Pharmacophore Models for Virtual Screening. 101-110 - Teng-Zhi Long, Shao-Hua Shi, Shao Liu, Ai-Ping Lu, Zhao-Qian Liu, Min Li, Tingjun Hou, Dong-Sheng Cao:
Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches. 111-125 - Omri Wolk, Amiram Goldblum:
Predicting the Likelihood of Molecules to Act as Modulators of Protein-Protein Interactions. 126-137 - Daniel Sethio, Poongavanam Vasanthanathan, Ruisheng Xiong, Mohit Tyagi, Duc Duy Vo, Roland Lindh, Jan Kihlberg:
Simulation Reveals the Chameleonic Behavior of Macrocycles. 138-146 - Paul L. Türtscher, Markus Reiher:
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach. 147-160 - Mirko Paulikat, Daniele Vitone, Florian Karl Schackert, Nils Schuth, Alessandra Barbanente, GiovanniMaria Piccini, Emiliano Ippoliti, Giulia Rossetti, Adam H. Clark, Maarten Nachtegaal, Michael Haumann, Holger Dau, Paolo Carloni, Silvano Geremia, Rita De Zorzi, Liliana Quintanar, Fabio Arnesano:
Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes. 161-172 - Chen Qian, Xin Zhou, Jessica Rehmel, James P. Steele, Kjell A. Svensson, James P. Beck, Erik J. Hembre, Junliang Hao:
Ensemble Docking Approach to Mitigate Pregnane X Receptor-Mediated CYP3A4 Induction Risk. 173-186 - Andrey I. Frolov, Sunay V. Chankeshwara, Zeyed Abdulkarim, Gian Marco Ghiandoni:
pIChemiSt ─ Free Tool for the Calculation of Isoelectric Points of Modified Peptides. 187-196 - Oriol Gracia Carmona, Chris Oostenbrink:
Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom. 197-207 - Chythra J. N., Sairam S. Mallajosyula:
Impact of Polarization on the Ring Puckering Dynamics of Hexose Monosaccharides. 208-223 - Nibedita Ray Chaudhuri, Shubhra Ghosh Dastidar:
Allosteric Boost by TAB1 on the TAK1 Kinase Favorably Sculpts the Thermodynamic Landscape of Activation. 224-239 - Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi, Akinori Kidera:
Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease. 240-250 - Francesco Pettini, Carmen Domene, Simone Furini:
Early Steps in C-Type Inactivation of the hERG Potassium Channel. 251-258 - Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta:
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. 259-269 - Leslie Sánchez, Fabiola E. Medina, Fernanda Mendoza, Camilo Febres-Molina, Gonzalo A. Jaña:
Elucidation of the Reaction Mechanism of Cavia porcellus l-Asparaginase: A QM/MM Study. 270-280 - Till El Harrar, Holger Gohlke:
Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. 281-298 - Anastasiia Delova, Raúl Losantos, Jérémy Pecourneau, Yann Bernhard, Maxime Mourer, Andreea Pasc, Antonio Monari:
Perturbation of Lipid Bilayers by Biomimetic Photoswitches Based on Cyclocurcumin. 299-307 - Yuying Liu, Ying Wang, Yu Zhang, Yu Zou, Guanghong Wei, Feng Ding, Yunxiang Sun:
Structural Perturbation of Monomers Determines the Amyloid Aggregation Propensity of Calcitonin Variants. 308-320 - Aristarc Suriñach, Adam Hospital, Yvonne Westermaier, Luis Jordà, Sergi Orozco-Ruiz, Daniel Beltrán, Francesco Colizzi, Pau Andrio, Robert Soliva, Martí Municoy, Josep Lluis Gelpí, Modesto Orozco:
High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations. 321-334 - Jiahui Chen, Rui Wang, Yuta Hozumi, Gengzhuo Liu, Yuchi Qiu, Xiaoqi Wei, Guo-Wei Wei:
Emerging Dominant SARS-CoV-2 Variants. 335-342 - Luca Torielli, Stefano A. Serapian, Lara Mussolin, Elisabetta Moroni, Giorgio Colombo:
Integrating Protein Interaction Surface Prediction with a Fragment-Based Drug Design: Automatic Design of New Leads with Fragments on Energy Surfaces. 343-353 - Madelyn Smith, Pengfei Li:
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. 354-361 - Xiaoyue Ji, Hao Liu, Yangpeng Zhang, Jun Chen, Hai-Feng Chen:
Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning. 362-374 - Reem A. Alkhodier, Sushil Kumar Mishra, Robert J. Doerksen, David A. Colby:
Comparison of Conformational Analyses of Naturally Occurring Flavonoid-O-Glycosides with Unnatural Flavonoid-CF2-Glycosides Using Molecular Modeling. 375-386 - Marley L. Samways, Hannah E. Bruce Macdonald, Richard D. Taylor, Jonathan W. Essex:
Water Networks in Complexes between Proteins and FDA-Approved Drugs. 387-396 - Yan Liu, He Yan, Long-Chen Shen, Dong-Jun Yu:
Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation. 397-405 - Stefano Costanzi, Charlotte K. Slavick, Brent O. Hutcheson, Gregory D. Koblentz, Richard T. Cupitt:
Correction to "Lists of Chemical Warfare Agents and Precursors from International Nonproliferation Frameworks: Structural Annotation and Chemical Fingerprint Analysis". 406
Volume 63, Number 2, January 2023
- Diego Enry Barreto Gomes, Katia Galentino, Marion Sisquellas, Luca Monari, Cédric Bouysset, Marco Cecchini:
ChemFlow─From 2D Chemical Libraries to Protein-Ligand Binding Free Energies. 407-411 - Kristian Kríz, Lisa Schmidt, Alfred T. Andersson, Marie-Madeleine Walz, David van der Spoel:
An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation. 412-431 - Raghad Al-Jarf, Simon Tang, Douglas E. V. Pires, David B. Ascher:
embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules. 432-441 - Raya Stoyanova, Paul Maximilian Katzberger, Leonid Komissarov, Aous Khadhraoui, Lisa Sach-Peltason, Katrin Groebke Zbinden, Torsten Schindler, Nenad Manevski:
Computational Predictions of Nonclinical Pharmacokinetics at the Drug Design Stage. 442-458 - Cesare Roncaglia, Riccardo Ferrando:
Machine Learning Assisted Clustering of Nanoparticle Structures. 459-473 - Iori Azuma, Tadahaya Mizuno, Hiroyuki Kusuhara:
NRBdMF: A Recommendation Algorithm for Predicting Drug Effects Considering Directionality. 474-483 - Ye Buehler, Jean-Louis Reymond:
Molecular Framework Analysis of the Generated Database GDB-13s. 484-492 - Yangcheng Ai, Zichao Yang, Zilong Yang, Shanhe Wan, Chunhui Huang, Chuan Huang, Mingxia Li, Zhonghuang Li, Jiajie Zhang, Tingting Zhang:
Discovery and Computational Studies of Potent Covalent Kinase Inhibitors with α-Substituent Electrophiles Targeting Cysteine. 493-506 - Sebastián Adolfo Cuesta, Martín Moreno, Romina A. López, José Ramón Mora, José Luis Paz, Edgar Márquez:
ElectroPredictor: An Application to Predict Mayr's Electrophilicity E through Implementation of an Ensemble Model Based on Machine Learning Algorithms. 507-521 - Reecan J. Juarez, Yaoyukun Jiang, Matthew Tremblay, Qianzhen Shao, A. James Link, Zhongyue J. Yang:
LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling. 522-530 - Luca Mollica, Gabriele Giachin:
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study. 531-545 - Alexander Zlobin, Julia Belyaeva, Andrey V. Golovin:
Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms. 546-560 - Yishui Li, Runduo Liu, Jie Liu, Haibin Luo, Chengkun Wu, Zhe Li:
An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations. 561-570 - Namita Dube, Sabab Hasan Khan, Riley Sasse, C. Denise Okafor:
Identification of an Evolutionarily Conserved Allosteric Network in Steroid Receptors. 571-582 - Filipp Gusev, Evgeny Gutkin, Maria G. Kurnikova, Olexandr Isayev:
Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling. 583-594 - Federico N. Pedron, Andresa Messias, Ari Zeida, Adrian E. Roitberg, Dario A. Estrin:
Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field. 595-604 - Xiaokun Hong, Kaiyuan Song, Mueed Ur Rahman, Ting Wei, Yan Zhang, Lin-Tai Da, Hai-Feng Chen:
Phosphorylation Regulation Mechanism of β2 Integrin for the Binding of Filamin Revealed by Markov State Model. 605-618 - Jie Gao, Yaoliang Zhang, Lin Yu, Yuejuan Li, Shumin Liao, Jian Wang, Lijie Guan:
Identification of Enolase 1 as a Potential Target for Magnaporthe oryzae: Integrated Proteomic and Molecular Dynamics Simulation. 619-632 - Natasha Gupta Vergara, Megan Gatchel, Cameron F. Abrams:
Entropic Overcompensation of the N501Y Mutation on SARS-CoV-2 S Binding to ACE2. 633-642 - Ke Zuo, Riccardo Capelli, Giulia Rossetti, Rachel Nechushtai, Paolo Carloni:
Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET. 643-654 - Zakir Ali, Ambika Goyal, Ayush Jhunjhunwala, Abhijit Mitra, John F. Trant, Purshotam Sharma:
Structural and Energetic Features of Base-Base Stacking Contacts in RNA. 655-669 - Rojalin Pradhan, Sibarama Panigrahi, Prabhat K. Sahu:
Conformational Search for the Building Block of Proteins Based on the Gradient Gravitational Search Algorithm (ConfGGS) Using Force Fields: CHARMM, AMBER, and OPLS-AA. 670-690
Volume 63, Number 3, February 2023
- Fabio Urbina, Filippa Lentzos, Cédric Invernizzi, Sean Ekins:
Preventing AI From Creating Biochemical Threats. 691-694 - Yan A. Ivanenkov, Daniil Polykovskiy, Dmitry Bezrukov, Bogdan Zagribelnyy, Vladimir Aladinskiy, Petrina Kamya, Alex Aliper, Feng Ren, Alex Zhavoronkov:
Chemistry42: An AI-Driven Platform for Molecular Design and Optimization. 695-701 - Cécile Hilpert, Louis Beranger, Paulo Cesar Telles de Souza, Petteri A. Vainikka, Vincent Nieto, Siewert J. Marrink, Luca Monticelli, Guillaume Launay:
Facilitating CG Simulations with MAD: The MArtini Database Server. 702-710 - Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Götz, Kenneth M. Merz Jr.:
Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units. 711-717 - Mateusz K. Bieniek, Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney:
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal. 718-724 - Adem R. N. Aouichaoui, Fan Fan, Seyed Soheil Mansouri, Jens Abildskov, Gürkan Sin:
Combining Group-Contribution Concept and Graph Neural Networks Toward Interpretable Molecular Property Models. 725-744 - Lincan Fang, Xiaomi Guo, Milica Todorovic, Patrick Rinke, Xi Chen:
Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization. 745-752 - Frank W. Marrs, Jack V. Davis, Alexandra C. Burch, Geoffrey W. Brown, Nicholas Lease, Patricia L. Huestis, Marc J. Cawkwell, Virginia W. Manner:
Chemical Descriptors for a Large-Scale Study on Drop-Weight Impact Sensitivity of High Explosives. 753-769 - Yixiang Ruan, Sen Lin, Yiming Mo:
AROPS: A Framework of Automated Reaction Optimization with Parallelized Scheduling. 770-781 - Donghan Wang, Wenze Li, Xu Dong, Hongzhi Li, Lihong Hu:
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion. 782-793 - Kohei Nemoto, Hiromasa Kaneko:
De Novo Direct Inverse QSPR/QSAR: Chemical Variational Autoencoder and Gaussian Mixture Regression Models. 794-805 - Yufeng Liu, Zhenyu Li:
Predict Ionization Energy of Molecules Using Conventional and Graph-Based Machine Learning Models. 806-814 - Yuqing Yang, Dongping Liu, Zhendong Hua, Peng Xu, Youmei Wang, Bin Di, Jun Liao, Mengxiang Su:
Machine Learning-Assisted Rapid Screening of Four Types of New Psychoactive Substances in Drug Seizures. 815-825 - Adnan Khan, Jamal Uddin, Farman Ali, Harish Kumar, Wajdi Alghamdi, Aftab Ahmad:
AFP-SPTS: An Accurate Prediction of Antifreeze Proteins Using Sequential and Pseudo-Tri-Slicing Evolutionary Features with an Extremely Randomized Tree. 826-834 - Haiping Zhang, Konda Mani Saravanan, Yanjie Wei, Yang Jiao, Yang Yang, Yi Pan, Xuli Wu, John Z. H. Zhang:
Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening. 835-845 - Tuan Xu, Md Kabir, Srilatha Sakamuru, Pranav Shah, Elias C. Padilha, Deborah K. Ngan, Menghang Xia, Xin Xu, Anton Simeonov, Ruili Huang:
Predictive Models for Human Cytochrome P450 3A7 Selective Inhibitors and Substrates. 846-855 - Seungchan An, Seok Young Hwang, Junpyo Gong, Sungjin Ahn, In Guk Park, Soyeon Oh, Young-Won Chin, Minsoo Noh:
Computational Prediction of the Phenotypic Effect of Flavonoids on Adiponectin Biosynthesis. 856-869 - Sneha Thomas, Kevin S. Silmore, Piyush Sharma, Ananth Govind Rajan:
Enumerating Stable Nanopores in Graphene and Their Geometrical Properties Using the Combinatorics of Hexagonal Lattices. 870-881 - Álvaro Pérez-Barcia, Gustavo Cárdenas, Juan J. Nogueira, Marcos Mandado:
Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis. 882-897 - Francesca Peccati, Sara Alunno-Rufini, Gonzalo Jiménez-Osés:
Accurate Prediction of Enzyme Thermostabilization with Rosetta Using AlphaFold Ensembles. 898-909 - Abhishek Acharya, Ishan Ghai, Claudio Piselli, Jigneshkumar Dahyabhai Prajapati, Roland Benz, Mathias Winterhalter, Ulrich Kleinekathöfer:
Conformational Dynamics of Loop L3 in OmpF: Implications toward Antibiotic Translocation and Voltage Gating. 910-927 - Efpraxia Tzortzini, Robin A. Corey, Antonios Kolocouris:
Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A2A and A1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations. 928-949 - Santiago Movilla, Sergio Martí, Maite Roca, Vicent Moliner:
Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer's Disease. 950-958 - Krishna Prasad Ghanta, Souvik Mondal, Timir Hajari, Sanjoy Bandyopadhyay:
Impact of an Ionic Liquid on Amino Acid Side Chains: A Perspective from Molecular Simulation Studies. 959-972 - Patrice Koehl, Arseniy V. Akopyan, Herbert Edelsbrunner:
Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives. 973-985 - Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Xudong Yang, Chengwen Liu, Zhifeng Jing, Juhoon Lee, Matthew Harger, Ally K. Smith, Miguel Espinoza, Hou-Fu Guo, Jonathan M. Kurie, Kevin N. Dalby, Pengyu Y. Ren, G. Andrés Cisneros:
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. 986-1001 - Saikat Pal, Amit Kumar, Harish Vashisth:
Role of Dynamics and Mutations in Interactions of a Zinc Finger Antiviral Protein with CG-rich Viral RNA. 1002-1011 - Adam Stasiulewicz, Anna Lesniak, Magdalena Bujalska-Zadrozny, Tomasz Pawinski, Joanna I. Sulkowska:
Identification of Novel CB2 Ligands through Virtual Screening and In Vitro Evaluation. 1012-1027 - Horrick Sharma, Pragya Sharma, Uzziah Urquiza, Lerin R. Chastain, Michael A. Ihnat:
Exploration of a Large Virtual Chemical Space: Identification of Potent Inhibitors of Lactate Dehydrogenase-A against Pancreatic Cancer. 1028-1043 - Jun Hu, Wen-Wu Zeng, Ning-Xin Jia, Muhammad Arif, Dong-Jun Yu, Gui-Jun Zhang:
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm. 1044-1057 - Kai Kang, Lei Wang, Chen Song:
ProtRAP: Predicting Lipid Accessibility Together with Solvent Accessibility of Proteins in One Run. 1058-1065 - Ran Liu, Xiang Liu, Jie Wu:
Persistent Path-Spectral (PPS) Based Machine Learning for Protein-Ligand Binding Affinity Prediction. 1066-1075 - Xue-Qiang Fan, Bing Lin, Jun Hu, Zhong-Yi Guo:
I-DNAN6mA: Accurate Identification of DNA N6-Methyladenine Sites Using the Base-Pairing Map and Deep Learning. 1076-1086
Volume 63, Number 4, February 2023
- Darya Stepanenko, Stephanie Budhan, Carlos Simmerling:
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. 1087-1092 - Jan-Oliver Felix Kapp-Joswig, Bettina G. Keller:
CommonNNClustering─A Python Package for Generic Common-Nearest-Neighbor Clustering. 1093-1098 - Jonathan G. M. Conn, James W. Carter, Justin J. A. Conn, Vigneshwari Subramanian, Andrew Baxter, Ola Engkvist, Antonio Llinàs, Ekaterina Ratkova, Stephen D. Pickett, James L. McDonagh, David S. Palmer:
Blinded Predictions and Post Hoc Analysis of the Second Solubility Challenge Data: Exploring Training Data and Feature Set Selection for Machine and Deep Learning Models. 1099-1113 - Mohammadamin Tavakoli, Yin Ting T. Chiu, Pierre Baldi, Ann Marie Carlton, David Van Vranken:
RMechDB: A Public Database of Elementary Radical Reaction Steps. 1114-1123 - Sergei A. Evteev, Alexey V. Ereshchenko, Yan A. Ivanenkov:
SiteRadar: Utilizing Graph Machine Learning for Precise Mapping of Protein-Ligand-Binding Sites. 1124-1132 - Jintu Zhang, Haotian Zhang, Zhixin Qin, Yu Kang, Xin Hong, Tingjun Hou:
Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials. 1133-1142 - Jiali Guo, Ming Sun, Xueyan Zhao, Chaojie Shi, Haoming Su, Yanzhi Guo, Xuemei Pu:
General Graph Neural Network-Based Model To Accurately Predict Cocrystal Density and Insight from Data Quality and Feature Representation. 1143-1156 - José Manuel Vásquez-Pérez, Luis Ángel Zárate-Hernández, Carlos Zepactonal Gómez-Castro, Uriel Alejandro Nolasco-Hernández:
A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters. 1157-1165 - Benjamin I. Tingle, Khanh G. Tang, Mar Castanon, John J. Gutierrez, Munkhzul Khurelbaatar, Chinzorig Dandarchuluun, Yurii S. Moroz, John J. Irwin:
ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery. 1166-1176 - Mengxian Yu, Yajuan Shi, Qingzhu Jia, Qiang Wang, Zheng-Hong Luo, Fangyou Yan, Yin-Ning Zhou:
Ring Repeating Unit: An Upgraded Structure Representation of Linear Condensation Polymers for Property Prediction. 1177-1187 - Bumjoon Seo, Brett M. Savoie:
Evidence That Less Can Be More for Transferable Force Fields. 1188-1195 - Zoe Li, Kevin C. Chan, Jonathan D. Nickels, Xiaolin Cheng:
Molecular Dynamics Refinement of Open State Serotonin 5-HT3A Receptor Structures. 1196-1207 - Sara Gómez, Piero Lafiosca, Franco Egidi, Tommaso Giovannini, Chiara Cappelli:
UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA. 1208-1217 - Brad Crawford, Umesh Timalsina, Co D. Quach, Nicholas C. Craven, Justin B. Gilmer, Clare McCabe, Peter T. Cummings, Jeffrey J. Potoff:
MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC. 1218-1228 - Lokesh Baweja, Jeff Wereszczynski:
Conformational and Thermodynamic Differences Underlying Wild-Type and Mutant Eleven-Nineteen-Leukemia YEATS Domain Specificity for Epigenetic Marks. 1229-1238 - Timofey V. Losev, Igor S. Gerasimov, Maria V. Panova, Alexey A. Lisov, Yana R. Abdyusheva, Polina V. Rusina, Eugenia Zaletskaya, Oleg V. Stroganov, Michael G. Medvedev, Fedor N. Novikov:
Quantum Mechanical-Cluster Approach to Solve the Bioisosteric Replacement Problem in Drug Design. 1239-1248 - Veronika Temml, Jakub Kollár, Theresa Schönleitner, Anna Höll, Daniela Schuster, Zsófia Kutil:
Combination of In Silico and In Vitro Screening to Identify Novel Glutamate Carboxypeptidase II Inhibitors. 1249-1259 - Raffaele Fiorentini, Thomas Tarenzi, Raffaello Potestio:
Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins. 1260-1275 - Mohammad Khavani, Aliyeh Mehranfar, Mohammad R. K. Mofrad:
On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study. 1276-1292 - Florian Karl Schackert, Johann Biedermann, Saeid Abdolvand, Sonja Minniberger, Chen Song, Andrew J. R. Plested, Paolo Carloni, Han Sun:
Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel. 1293-1300 - Kemel Arafet, Laura Scalvini, Francesca Galvani, Sergio Martí, Vicent Moliner, Marco Mor, Alessio Lodola:
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents. 1301-1312 - Lihua Dong, Yongjun Liu:
Catalytic Mechanism of Pyridoxal 5′-Phosphate-Dependent Aminodeoxychorismate Lyase: A Computational QM/MM Study. 1313-1322 - Pengyu Wang, Jun Zhang, Shengyu Zhang, Diannan Lu, Yushan Zhu:
Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes. 1323-1337 - Jeisson D. Corredor, Camilo Febres-Molina, Gonzalo A. Jaña, Verónica A. Jiménez:
Insight into the Role of Active Site Protonation States and Water Molecules in the Catalytic Inhibition of DPP4 by Vildagliptin. 1338-1350 - Viet Hoang Man, Xibing He, Fengyang Han, Lianjin Cai, Luxuan Wang, Taoyu Niu, Jingchen Zhai, Beihong Ji, Jie Gao, Junmei Wang:
Phosphorylation at Ser289 Enhances the Oligomerization of Tau Repeat R2. 1351-1361 - Zheng Zhao, Niraja Bohidar, Philip E. Bourne:
Analysis of KRAS-Ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics. 1362-1370 - Naila Zaman, Syed Sikander Azam:
Quantum Dynamics and Bi Metal Force Field Parameterization Yielding Significant Antileishmanial Targets. 1371-1385 - Sergio Alejandro Poveda-Cuevas, Fernando Luís Barroso da Silva, Catherine Etchebest:
NS1 from Two Zika Virus Strains Differently Interact with a Membrane: Insights to Understand Their Differential Virulence. 1386-1400
Volume 63, Number 5, March 2023
- Viet-Khoa Tran-Nguyen, Pedro J. Ballester:
Beware of Simple Methods for Structure-Based Virtual Screening: The Critical Importance of Broader Comparisons. 1401-1405 - Bharath Raghavan, Florian K. Schackert, Andrea Levy, Sophia K. Johnson, Emiliano Ippoliti, Davide Mandelli, Jógvan Magnus Haugaard Olsen, Ursula Rothlisberger, Paolo Carloni:
MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations. 1406-1412 - Steve Agajanian, Mohammed Alshahrani, Fang Bai, Peng Tao, Gennady M. Verkhivker:
Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. 1413-1428 - Yeajee Kwon, Sera Park, Jaeok Lee, Jiyeon Kang, Hwa Jeong Lee, Wan Kyu Kim:
BEAR: A Novel Virtual Screening Method Based on Large-Scale Bioactivity Data. 1429-1437 - Rajendra P. Joshi, Katherine J. Schultz, Jesse William Wilson, Agustin Kruel, Rohith Anand Varikoti, Chathuri J. Kombala, Daniel W. Kneller, Stephanie Galanie, Gwyndalyn Phillips, Qiu Zhang, Leighton Coates, Jyothi Parvathareddy, Surekha Surendranathan, Ying Kong, Austin Clyde, Arvind Ramanathan, Colleen B. Jonsson, Kristoffer R. Brandvold, Mowei Zhou, Martha S. Head, Andrey Kovalevsky, Neeraj Kumar:
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2. 1438-1453 - Esteban Marques, Stefan De Gendt, Geoffrey Pourtois, Michiel J. van Setten:
Improving Accuracy and Transferability of Machine Learning Chemical Activation Energies by Adding Electronic Structure Information. 1454-1461 - Andrew D. McNaughton, Rajendra P. Joshi, Carter R. Knutson, Fnu Anubhav, Kevin J. Luebke, Jeremiah P. Malerich, Peter B. Madrid, Neeraj Kumar:
Machine Learning Models for Predicting Molecular UV-Vis Spectra with Quantum Mechanical Properties. 1462-1471 - Zailiang Zhu, Bozheng Dou, Yukang Cao, Jian Jiang, Yueying Zhu, Dong Chen, Hongsong Feng, Jie Liu, Ben-gong Zhang, Tianshou Zhou, Guo-Wei Wei:
TIDAL: Topology-Inferred Drug Addiction Learning. 1472-1489 - Renne Leini, Tatu Pantsar:
In Silico Evaluation of the Thr58-Associated Conserved Water with KRAS Switch-II Pocket Binders. 1490-1505 - Luan Carvalho Martins, Renata Barbosa de Oliveira, Jerônimo Lameira, Rafaela Salgado Ferreira:
Experimental and Computational Study of Aryl-thiosemicarbazones Inhibiting Cruzain Reveals Reversible Inhibition and a Stepwise Mechanism. 1506-1520 - Inacrist Geronimo, Pietro Vidossich, Marco de Vivo:
On the Role of Molecular Conformation of the 8-Oxoguanine Lesion in Damaged DNA Processing by Polymerases. 1521-1528 - Yutaka Maruyama, Ryo Igarashi, Yoshitaka Ushiku, Ayori Mitsutake:
Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation. 1529-1541 - Souvik Mondal, Krishna Prasad Ghanta, Sanjoy Bandyopadhyay:
Microscopic Understanding of the Conformational Stability of the Aggregated Nonamyloid β Components of α-Synuclein. 1542-1555 - Beata Dulko-Smith, Pedro Ojeda-May, Jörgen Ådén, Magnus Wolf-Watz, Kwangho Nam:
Mechanistic Basis for a Connection between the Catalytic Step and Slow Opening Dynamics of Adenylate Kinase. 1556-1569 - Sweta Pradhan, Rajendra Rath, Mithun Biswas:
GB1 Dimerization in Crowders: A Multiple Resolution Approach. 1570-1577 - Asma Gholami, Dariush Minai-Tehrani, Sayyed Jalil Mahdizadeh, Patricia Saenz-Méndez, Leif A. Eriksson:
Structural Insights into Pseudomonas aeruginosa Exotoxin A-Elongation Factor 2 Interactions: A Molecular Dynamics Study. 1578-1591 - Ya Gao, Göran Widmalm, Wonpil Im:
Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Capsular Polysaccharides. 1592-1601 - Ge Song, Bozitao Zhong, Bo Zhang, Ashfaq Ur Rehman, Hai-Feng Chen:
Phosphorylation Modification Force Field FB18CMAP Improving Conformation Sampling of Phosphoproteins. 1602-1614 - Hong-Quan Xu, Wei Zhang, Ying Zhou, Zi-Xuan Yue, Tian-Ci Yan, Yuanyuan Zhang, Yu-Hong Liu, Yan-Feng Hong, Shuiping Liu, Feng Zhu, Lin Tao:
Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics. 1615-1625 - Wei Hu, Wei Zhang, Ying Zhou, Yongchao Luo, Xiuna Sun, Huimin Xu, Shuiyang Shi, Teng Li, Yichao Xu, Qianqian Yang, Yunqing Qiu, Feng Zhu, Haibin Dai:
MecDDI: Clarified Drug-Drug Interaction Mechanism Facilitating Rational Drug Use and Potential Drug-Drug Interaction Prediction. 1626-1636 - Dmitrij Rappoport, Adrian Jinich:
Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves. 1637-1648
Volume 63, Number 6, March 2023
- Cayque Monteiro Castro Nascimento, André Silva Pimentel:
Do Large Language Models Understand Chemistry? A Conversation with ChatGPT. 1649-1655 - Yuqi Zhang, Márton Vass, Da Shi, Esam Abualrous, Jennifer M. Chambers, Nikita Chopra, Christopher Higgs, Koushik Kasavajhala, Hubert Li, Prajwal Nandekar, Hideyuki Sato, Edward B. Miller, Matthew P. Repasky, Steven V. Jerome:
Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery. 1656-1667 - Anna M. Díaz-Rovira, Helena Martín, Thijs Beuming, Lucía Díaz, Victor Guallar, Soumya S. Ray:
Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures. 1668-1674 - Noah R. Flynn, S. Joshua Swamidass:
Message Passing Neural Networks Improve Prediction of Metabolite Authenticity. 1675-1694 - Matthew R. Masters, Amr H. Mahmoud, Yao Wei, Markus A. Lill:
Deep Learning Model for Efficient Protein-Ligand Docking with Implicit Side-Chain Flexibility. 1695-1707 - Kamal Choudhary, Ramya Gurunathan, Brian DeCost, Adam J. Biacchi:
AtomVision: A Machine Vision Library for Atomistic Images. 1708-1722 - Hamid Teimouri, Angela Medvedeva, Anatoly B. Kolomeisky:
Bacteria-Specific Feature Selection for Enhanced Antimicrobial Peptide Activity Predictions Using Machine-Learning Methods. 1723-1733 - Emma P. Tysinger, Brajesh K. Rai, Anton V. Sinitskiy:
Can We Quickly Learn to "Translate" Bioactive Molecules with Transformer Models? 1734-1744 - Brandon J. Bongers, Huub J. Sijben, Peter B. R. Hartog, Andrey Tarnovskiy, Adriaan P. IJzerman, Laura H. Heitman, Gerard J. P. van Westen:
Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors. 1745-1755 - Zheyu Hu, Yaolin Guo, Zhen Liu, Diwei Shi, Yifan Li, Yu Hu, Moran Bu, Kan Luo, Jian He, Chong Wang, Shiyu Du:
AisNet: A Universal Interatomic Potential Neural Network with Encoded Local Environment Features. 1756-1765 - Marianne Rooman, Fabrizio Pucci:
Estimating the Vertical Ionization Potential of Single-Stranded DNA Molecules. 1766-1775 - Mary Pitman, David F. Hahn, Gary Tresadern, David L. Mobley:
To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough. 1776-1793 - Emília P. Barros, Benjamin Ries, Candide Champion, Salomé Rieder, Sereina Riniker:
Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities. 1794-1805 - Katarzyna Walczewska-Szewc, Wieslaw Nowak:
Structural Insights into ATP-Sensitive Potassium Channel Mechanics: A Role of Intrinsically Disordered Regions. 1806-1818 - Saheb Dutta, Amalendu Chandra:
A Multiple Proton Transfer Mechanism for the Charging Step of the Aminoacylation Reaction at the Active Site of Aspartyl tRNA Synthetase. 1819-1832
Volume 63, Number 7, April 2023
- Xiaolin Pan, Fanyu Zhao, Yueqing Zhang, Xingyu Wang, Xudong Xiao, John Z. H. Zhang, Changge Ji:
MolTaut: A Tool for the Rapid Generation of Favorable Tautomer in Aqueous Solution. 1833-1840 - Samuel Genheden, Per-Ola Norrby, Ola Engkvist:
AiZynthTrain: Robust, Reproducible, and Extensible Pipelines for Training Synthesis Prediction Models. 1841-1846 - Nikita Ionov, Dmitry S. Druzhilovskiy, Dmitry Filimonov, Vladimir Poroikov:
Phyto4Health: Database of Phytocomponents from Russian Pharmacopoeia Plants. 1847-1851 - Andrew J. Hoover, Martin Spale, Brian Lahue, Danny A. Bitton:
Matcher: An Open-Source Application for Translating Large Structure/Property Data Sets into Insights for Drug Design. 1852-1857 - Althea T. Hansel-Harris, Diogo Santos-Martins, Niccolò Bruciaferri, Andreas F. Tillack, Matthew Holcomb, Stefano Forli:
Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results. 1858-1864 - Vishu Gupta, Kamal Choudhary, Yuwei Mao, Kewei Wang, Francesca Tavazza, Carelyn Campbell, Wei-keng Liao, Alok N. Choudhary, Ankit Agrawal:
MPpredictor: An Artificial Intelligence-Driven Web Tool for Composition-Based Material Property Prediction. 1865-1871 - Max Müller, Alexander Hagg, Robin Strickstrock, Marco Hülsmann, Alexander Asteroth, Karl N. Kirschner, Dirk Reith:
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization. 1872-1881 - Dibyajyoti Das, Broto Chakrabarty, Rajgopal Srinivasan, Arijit Roy:
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures. 1882-1893 - Zaiyun Lin, Shiqiu Yin, Lei Shi, Wenbiao Zhou, Yingsheng J. Zhang:
G2GT: Retrosynthesis Prediction with Graph-to-Graph Attention Neural Network and Self-Training. 1894-1905 - Zaw-Myo Win, Allen M. Y. Cheong, W. Scott Hopkins:
Using Machine Learning To Predict Partition Coefficient (Log P) and Distribution Coefficient (Log D) with Molecular Descriptors and Liquid Chromatography Retention Time. 1906-1913 - Fernando Jaume-Santero, Alban Bornet, Alain Valery, Nona Naderi, David Vicente Alvarez, Dimitrios Proios, Anthony Yazdani, Colin Bournez, Thomas Fessard, Douglas Teodoro:
Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios. 1914-1924 - Yujie Qian, Jiang Guo, Zhengkai Tu, Zhening Li, Connor W. Coley, Regina Barzilay:
MolScribe: Robust Molecular Structure Recognition with Image-to-Graph Generation. 1925-1934 - Mehdi Khashei, Erfan Nazgouei, Negar Bakhtiarvand:
Intelligent Discrete Deep Learning Based Classification Methodology in Chemometrics. 1935-1946 - Gregory W. Kyro, Rafael I. Brent, Victor S. Batista:
HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Prediction. 1947-1960 - Jiuyang Zhao, Shu Huang, Jacqueline M. Cole:
OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain. 1961-1981 - Ji Ding, Shidi Tang, Zheming Mei, Lingyue Wang, Qinqin Huang, Haifeng Hu, Ming Ling, Jiansheng Wu:
Vina-GPU 2.0: Further Accelerating AutoDock Vina and Its Derivatives with Graphics Processing Units. 1982-1998 - Jeronimo F. Silva, Guilherme S. L. Fabris, Julio R. Sambrano, Anderson R. Albuquerque, Ary S. Maia:
TopIso3D Viewer: Enhancing Topological Analysis through 3D Isosurfaces. 1999-2013 - Alessandro Nicoli, Franziska Haag, Patrick Marcinek, Ruiming He, Johanna Kreißl, Jörg Stein, Alessandro Marchetto, Andreas Dunkel, Thomas Hofmann, Dietmar Krautwurst, Antonella Di Pizio:
Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1. 2014-2029 - Valerie Welborn, William R. Archer, Michael D. Schulz:
Characterizing Ion-Polymer Interactions in Aqueous Environment with Electric Fields. 2030-2036 - Yu Zhao, Menglu Cui, Yongkang Lyu, Wen Gao, Xixi Cui, Changzhe Zhang, Qingtian Meng:
External Electric Field Effects on AFM-like Magnetism in Nitroxide-Functionalized C+:C Base Pair. 2037-2046 - Werner Treptow:
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands. 2047-2057 - Arup Mondal, G. V. T. Swapna, Maria M. Lopez, Laura Klang, Jingzhou Hao, Lichung Ma, Monica J. Roth, Gaetano T. Montelione, Alberto Perez:
Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations. 2058-2072 - Goutam Mukherjee, Abdennour Braka, Sangwook Wu:
Quantifying Functional-Group-like Structural Fragments in Molecules and Its Applications in Drug Design. 2073-2083 - Metehan Ilter, Eric Schulze-Niemand, Michael Naumann, Matthias Stein:
Structural Dynamics of Lys11-Selective Deubiquitinylase Cezanne-1 during the Catalytic Cycle. 2084-2094 - Bidhya Thapa, Narayan P. Adhikari, Purushottam B. Tiwari, Prem Chapagain:
A 5′-Flanking C/G Pair at the Core Region Enhances the Recognition and Binding of Kaiso to Methylated DNA. 2095-2103 - Nopawit Khamto, Kraikrit Utama, Suriya Tateing, Padchanee Sangthong, Puracheth Rithchumpon, Nathaporn Cheechana, Aroonchai Saiai, Natthawat Semakul, Winita Punyodom, Puttinan Meepowpan:
Discovery of Natural Bisbenzylisoquinoline Analogs from the Library of Thai Traditional Plants as SARS-CoV-2 3CLPro Inhibitors: In Silico Molecular Docking, Molecular Dynamics, and In Vitro Enzymatic Activity. 2104-2121 - Rajdip Misra, Anupam Maity, Shubham Kundu, Mrinmay Bhunia, Banadipa Nanda, Nakul C. Maiti, Uttam Pal:
Loop Dynamics and Conformational Flexibility in Dengue Serine Protease Activity: Noninvasive Perturbation by Solvent Exchange. 2122-2132 - Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás:
Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. 2133-2146 - Mateusz Marcisz, Sergey A. Samsonov:
Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans. 2147-2157 - Olivia Garland, Anh-Tien Ton, Shoeib Moradi, Jason R. Smith, Suzana Kovacic, Kurtis Ng, Mohit Pandey, Fuqiang Ban, Jaeyong Lee, Marija Vuckovic, Liam J. Worrall, Robert N. Young, Ralph Pantophlet, Natalie C. J. Strynadka, Artem Cherkasov:
Large-Scale Virtual Screening for the Discovery of SARS-CoV-2 Papain-like Protease (PLpro) Non-covalent Inhibitors. 2158-2169 - Ernest Awoonor-Williams, Andrei A. Golosov, Viktor Hornak:
Benchmarking In Silico Tools for Cysteine pKa Prediction. 2170-2180 - Ziad Fakhoury, Gabriele C. Sosso, Scott Habershon:
Generating Protein Folding Trajectories Using Contact-Map-Driven Directed Walks. 2181-2195 - Paween Mahinthichaichan, Ruibin Liu, Quynh N. Vo, Christopher R. Ellis, Lidiya Stavitskaya, Jana Shen:
Structure-Kinetics Relationships of Opioids from Metadynamics and Machine Learning Analysis. 2196-2206 - Samiran Sen, Morten Ledum, Sigbjørn Løland Bore, Michele Cascella:
Soft Matter under Pressure: Pushing Particle-Field Molecular Dynamics to the Isobaric Ensemble. 2207-2217 - Christian Kersten, Steven Clower, Fabian Barthels:
Hic Sunt Dracones: Molecular Docking in Uncharted Territories with Structures from AlphaFold2 and RoseTTAfold. 2218-2225 - Folorunsho Bright Omage, Andrea Madabeni, Amanda Resende Tucci, Pablo Andrei Nogara, Marco Bortoli, Alice dos Santos Rosa, Vivian Neuza dos Santos Ferreira, João Batista Teixeira da Rocha, Milene Dias Miranda, Laura Orian:
Diphenyl Diselenide and SARS-CoV-2: in silico Exploration of the Mechanisms of Inhibition of Main Protease (Mpro) and Papain-like Protease (PLpro). 2226-2239 - Jianan Li, Keisuke Yanagisawa, Masatake Sugita, Takuya Fujie, Masahito Ohue, Yutaka Akiyama:
CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. 2240-2250 - Kailong Li, Lijun Quan, Yelu Jiang, Hongjie Wu, Jian Wu, Yan Li, Yiting Zhou, Tingfang Wu, Qiang Lyu:
Simultaneous Prediction of Interaction Sites on the Protein and Peptide Sides of Complexes through Multilayer Graph Convolutional Networks. 2251-2262 - Yang Zhou, Junhao Li, Glib Baryshnikov, Yaoquan Tu:
Correction to "Unraveling the Abnormal Molecular Mechanism of Suicide Inhibition of Cytochrome P450 3A4". 2263-2264 - Patrick Bleiziffer, Kay Schaller, Sereina Riniker:
Correction to "Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations". 2265 - Derek van Tilborg, Alisa Alenicheva, Francesca Grisoni:
Correction to "Exposing the Limitations of Molecular Machine Learning with Activity Cliffs". 2266
Volume 63, Number 8, April 2023
- Claudio N. Cavasotto, Juan I. Di Filippo:
The Impact of Supervised Learning Methods in Ultralarge High-Throughput Docking. 2267-2280 - Yoona Yang, Michael S. Eldred, Judit Zádor, Habib N. Najm:
Multifidelity Neural Network Formulations for Prediction of Reactive Molecular Potential Energy Surfaces. 2281-2295 - Parisa Mollaei, Amir Barati Farimani:
Activity Map and Transition Pathways of G Protein-Coupled Receptor Revealed by Machine Learning. 2296-2304 - Labeeb Ali, Kaushik Sivaramakrishnan, Mohamed Shafi Kuttiyathil, Vignesh Chandrasekaran, Oday H. Ahmed, Mohammad Al-Harahsheh, Mohammednoor Altarawneh:
Prediction of Thermogravimetric Data in Bromine Captured from Brominated Flame Retardants (BFRs) in e-Waste Treatment Using Machine Learning Approaches. 2305-2320 - Tuan Xu, Shuaizhang Li, Andrew J. Li, Jinghua Zhao, Srilatha Sakamuru, Wenwei Huang, Menghang Xia, Ruili Huang:
Identification of Potent and Selective Acetylcholinesterase/Butyrylcholinesterase Inhibitors by Virtual Screening. 2321-2330 - Meenakshi Verma, Laxmikant Trivedi, Prema G. Vasudev:
Interaction Patterns of Pyrazolopyrimidines with Receptor Proteins. 2331-2344 - Yanqing Duan, Li Fu, Xiao-Chen Zhang, Teng-Zhi Long, Yuan-Hang He, Zhao-Qian Liu, Ai-Ping Lu, Yafeng Deng, Chang-Yu Hsieh, Tingjun Hou, Dong-Sheng Cao:
Improved GNNs for Log D7.4 Prediction by Transferring Knowledge from Low-Fidelity Data. 2345-2359 - Francois Berenger, Koji Tsuda:
3D-Sensitive Encoding of Pharmacophore Features. 2360-2369 - Robert M. Raddi, Yunhui Ge, Vincent A. Voelz:
BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations. 2370-2381 - Dahlia R. Weiss, Andrea Bortolato, Yongnian Sun, Xianmei Cai, Chon Lai, Sixuan Guo, Lihong Shi, Veerabahu Shanmugasundaram:
On Ternary Complex Stability in Protein Degradation: In Silico Molecular Glue Binding Affinity Calculations. 2382-2392 - Suvankar Ghosh, Tanumoy Sarkar, Sunanda Chatterjee, Priyadarshi Satpati:
Bridging Thermodynamics, Antimicrobial Activity, and pH Sensitivity of Cationic Membranolytic Heptapeptides-A Computational and Experimental Study. 2393-2408 - Xue-Li Hao, Ai-Min Ren, Liang Zhou:
Theoretical Studies and Design Strategies of Highly Efficient Two-Photon Excited Fluorescent Probes for Hydrogen Sulfide Detection through Simulation of Excited-State Dynamics. 2409-2418 - Phu K. Tang, Prabir Khatua, Vincenzo Carnevale, Sharon M. Loverde:
Exploration of the Nucleation Pathway for Supramolecular Fibers. 2419-2426 - Rohan Yuri Sanspeur, Javier Heras-Domingo, John R. Kitchin, Zachary W. Ulissi:
WhereWulff: A Semiautonomous Workflow for Systematic Catalyst Surface Reactivity under Reaction Conditions. 2427-2437 - Francesc Sabanés Zariquiey, Adrià Pérez, Maciej Majewski, Emilio Gallicchio, Gianni De Fabritiis:
Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series. 2438-2444 - Kira R. Mills, Hedieh Torabifard:
Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLCF Antiporter. 2445-2455 - Xiaoyue Ji, Xiaochen Cui, Zhengxin Li, Taeyoung Choi, Ying Wang, Wen Xiao, Yunshuo Zhao, Jinyin Zha, Jian Zhang, Hai-Feng Chen, Zhengtian Yu:
Research and Evaluation of the Allosteric Protein-Specific Force Field Based on a Pre-Training Deep Learning Model. 2456-2468 - Anupam Anand Ojha, Ambuj Srivastava, Lane W. Votapka, Rommie E. Amaro:
Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. 2469-2482 - Aarion Romany, Ruibin Liu, Shaoqi Zhan, Joseph Clayton, Jana Shen:
Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases. 2483-2494 - Cristina González Fernández, Christoph Öhlknecht, Matthias Diem, Yerko Escalona, Eugenio Bringas, Gabriel Moncalián, Chris Oostenbrink, Inmaculada Ortiz:
Insights into the Binding Mode of Lipid A to the Anti-lipopolysaccharide Factor ALFPm3 from Penaeus monodon: An In Silico Study through MD Simulations. 2495-2504 - Lauren Winkler, Thomas E. Cheatham:
Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide. 2505-2511 - Haohao Fu, Christophe Chipot, Xueguang Shao, Wensheng Cai:
Achieving Accurate Standard Protein-Protein Binding Free Energy Calculations through the Geometrical Route and Ergodic Sampling. 2512-2519 - Ernest Awoonor-Williams, Callum J. Dickson, Pascal Furet, Andrei A. Golosov, Viktor Hornak:
Leveraging Advanced In Silico Techniques in Early Drug Discovery: A Study of Potent Small-Molecule YAP-TEAD PPI Disruptors. 2520-2531 - Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Mohammad Akbari, Najmeh Salehi, Ali Masoudi-Nejad:
DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs. 2532-2545 - Mehrad Ansari, Andrew D. White:
Serverless Prediction of Peptide Properties with Recurrent Neural Networks. 2546-2553 - Afra Sabei, Talissa Gabriele Caldas Baia, Raphaël Saffar, Juliette Martin, Elisa Frezza:
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes. 2554-2572 - Torben Gutermuth, Jochen Sieg, Tim Stohn, Matthias Rarey:
Modeling with Alternate Locations in X-ray Protein Structures. 2573-2585 - Barbara Scalvini, Vahid Sheikhhassani, Nadine van de Brug, Laurens W. H. J. Heling, Jeremy D. Schmit, Alireza Mashaghi:
Circuit Topology Approach for the Comparative Analysis of Intrinsically Disordered Proteins. 2586-2602
Volume 63, Number 9, May 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Harvinder Singh, Anupam Raja, Ajay Prakash, Bikash Medhi:
Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulation Workflow Bridged to MM/PBSA, Based on Gromacs and Zenity-Dependent GUI for Beginners in MD Simulation Study. 2603-2608 - Camila M. Clemente, Luciana Capece, Marcelo A. Marti:
Best Practices on QM/MM Simulations of Biological Systems. 2609-2627 - Thi Tuyet Van Tran, Agung Surya Wibowo, Hilal Tayara, Kil To Chong:
Artificial Intelligence in Drug Toxicity Prediction: Recent Advances, Challenges, and Future Perspectives. 2628-2643 - Jack B. Greisman, Lindsay Willmore, Christine Y. Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter M. Nisonoff, Paul Maragakis, David E. Shaw:
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. 2644-2650 - Felix Teufel, Jan C. Refsgaard, Marina A. Kasimova, Kristine K. Deibler, Christian T. Madsen, Carsten Stahlhut, Mads Grønborg, Ole Winther, Dennis Madsen:
Deorphanizing Peptides Using Structure Prediction. 2651-2655 - Edison Mucllari, Vasily Zadorozhnyy, Qiang Ye, Duc Duy Nguyen:
Novel Molecular Representations Using Neumann-Cayley Orthogonal Gated Recurrent Unit. 2656-2666 - David Buterez, Jon Paul Janet, Steven J. Kiddle, Pietro Liò:
MF-PCBA: Multifidelity High-Throughput Screening Benchmarks for Drug Discovery and Machine Learning. 2667-2678 - Gao-Peng Ren, Ke-Jun Wu, Yuchen He:
Enhancing Molecular Representations Via Graph Transformation Layers. 2679-2688 - Maria J. Falaguera, Jordi Mestres:
Illuminating the Chemical Space of Untargeted Proteins. 2689-2698 - Stuart J. McElhany, Thomas J. Summers, Richard C. Shiery, David C. Cantu:
Analysis of the First Ion Coordination Sphere: A Toolkit to Analyze the Coordination Sphere of Ions. 2699-2706 - Bundit Kamsri, Bongkochawan Pakamwong, Paptawan Thongdee, Naruedon Phusi, Pharit Kamsri, Auradee Punkvang, Sombat Ketrat, Patchreenart Saparpakorn, Supa Hannongbua, Jidapa Sangswan, Khomson Suttisintong, Sanya Sureram, Prasat Kittakoop, Poonpilas Hongmanee, Pitak Santanirand, Jiraporn Leanpolchareanchai, Kirsty E. Goudar, James Spencer, Adrian J. Mulholland, Pornpan Pungpo:
Bioisosteric Design Identifies Inhibitors of Mycobacterium tuberculosis DNA Gyrase ATPase Activity. 2707-2718 - Kirill Shmilovich, Benson Chen, Theofanis Karaletsos, Mohammad M. Sultan:
DEL-Dock: Molecular Docking-Enabled Modeling of DNA-Encoded Libraries. 2719-2727 - Farzad Molani, Simon Webb, Art E. Cho:
Combining QM/MM Calculations with Classical Mining Minima to Predict Protein-Ligand Binding Free Energy. 2728-2734 - Benjamin I. Tingle, John J. Irwin:
Large-Scale Docking in the Cloud. 2735-2741 - Xinyu Xia, Yongli Gao:
Determining Reaction Paths by Evaluating Kinetic Isotopic Effects with Density Functional Theory: Example of Methane Thermogenesis. 2742-2747 - Matthew C. Chan, Diwakar Shukla:
The Effects of N-Linked Glycosylation on SLC6 Transporters. 2748-2758 - Xue Zhang, Xinyi Li, Yijing Wang, Xianghui Zhang, Yongjun Liu:
Computational Study of the Fe(II) and α-Ketoglutarate-Dependent Aryloxyalkanoate Dioxygenase (AAD-1) in the Degradation of the Herbicide 2,4-Dichlorophenoxyacetic Acid. 2759-2768 - Moses K. J. Chung, Ryan J. Miller, Borna Novak, Zhi Wang, Jay W. Ponder:
Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field. 2769-2782 - Irfan Muhammad, Ghulam Murtaza, Yi Zhao, Aysha Sarfraz Rizvi, Shangnan Fu, Xin Su, Feng Qu:
Exploration of the Interaction of Cadmium and Aptamer by Molecular Simulation and Development of Sensitive Capillary Zone Electrophoresis-Based Aptasensor. 2783-2793 - Zhengyue Zhang, Jirí Sponer, Giovanni Bussi, Vojtech Mlýnský, Petr Sulc, Chad R. Simmons, Nicholas Stephanopoulos, Miroslav Krepl:
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. 2794-2809 - João Morado, Paul N. Mortenson, J. Willem M. Nissink, Jonathan W. Essex, Chris-Kriton Skylaris:
Does a Machine-Learned Potential Perform Better Than an Optimally Tuned Traditional Force Field? A Case Study on Fluorohydrins. 2810-2827 - Shan Sun, Makoto Fushimi, Thomas Rossetti, Navpreet Kaur, Jacob Ferreira, Michael Miller, Jonathan Quast, Joop van den Heuvel, Clemens Steegborn, Lonny R. Levin, Jochen Buck, Robert W. Myers, Stacia Kargman, Nigel Liverton, Peter T. Meinke, David J. Huggins:
Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation. 2828-2841 - Francesca Galvani, Daniele Pala, Alberto Cuzzolin, Laura Scalvini, Alessio Lodola, Marco Mor, Andrea Rizzi:
Unbinding Kinetics of Muscarinic M3 Receptor Antagonists Explained by Metadynamics Simulations. 2842-2856 - Sridip Parui, James C. Robertson, Sandeep Somani, Gary Tresadern, Cong Liu, Ken A. Dill:
MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands. 2857-2865 - Luiz Carlos Saramago, Marcos V. Santana, Bárbara Figueira Gomes, Rafael Ferreira Dantas, Mario R. Senger, Pedro Henrique Oliveira Borges, Vivian Neuza dos Santos Ferreira, Alice dos Santos Rosa, Amanda Resende Tucci, Milene Dias Miranda, Petra Lukacik, Claire Strain-Damerell, C. David Owen, Martin A. Walsh, Sabrina Baptista Ferreira, Floriano Silva-Junior:
AI-Driven Discovery of SARS-CoV-2 Main Protease Fragment-like Inhibitors with Antiviral Activity In Vitro. 2866-2880 - Moran Zhou, Jiamin Sun, Zhuohang Yu, Zengrui Wu, Weihua Li, Guixia Liu, Lei Ma, Rui Wang, Yun Tang:
Investigation of Anti-Alzheimer's Mechanisms of Sarsasapogenin Derivatives by Network-Based Combining Structure-Based Methods. 2881-2894
Volume 63, Number 10, May 2023
- Samuel Boobier, Joseph C. Davies, Ivan N. Derbenev, Christopher M. Handley, Jonathan D. Hirst:
AI4Green: An Open-Source ELN for Green and Sustainable Chemistry. 2895-2901 - Steffen Wolf:
Predicting Protein-Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics: Current State and Challenges. 2902-2910 - Mercedes Alfonso-Prieto, Riccardo Capelli:
Machine Learning-Based Modeling of Olfactory Receptors in Their Inactive State: Human OR51E2 as a Case Study. 2911-2917 - Chien-Ting Kao, Chieh-Te Lin, Cheng-Li Chou, Chu-Chung Lin:
Fragment Linker Prediction Using the Deep Encoder-Decoder Network for PROTACs Drug Design. 2918-2927 - Hou Yee Choo, Junjie Wee, Cong Shen, Kelin Xia:
Fingerprint-Enhanced Graph Attention Network (FinGAT) Model for Antibiotic Discovery. 2928-2935 - Zhitao Cai, Tengzi Liu, Qiaoling Lin, Jiahao He, Xiaowei Lei, Fangfang Luo, Yandong Huang:
Basis for Accurate Protein pKa Prediction with Machine Learning. 2936-2947 - Xiang-Wei Zhu, Valery R. Polyakov, Krishna Bajjuri, Huiyong Hu, Andreas Maderna, Clare A. Tovee, Suzanna C. Ward:
Building Machine Learning Small Molecule Melting Points and Solubility Models Using CCDC Melting Points Dataset. 2948-2959 - Jyotsnamayee Nayak, Ashita Sood, Mahesh Kulharia, Suban K. Sahoo, Rajender Kumar:
Structural Distortion of β-Cyclodextrin Plays a Key Role in the pH-dependent Host-Guest Chemistry with Doxorubicin, Evident by the Electrochemical and Molecular Dynamics Approach. 2975-2982 - Evrim Arslan, Zeynep Pinar Haslak, Gerald Monard, Ilknur Dogan, Viktorya Aviyente:
Quantum Mechanical Prediction of Dissociation Constants for Thiazol-2-imine Derivatives. 2992-3004 - Rong Yang, Linhua Liu, Dansheng Jiang, Lei Liu, Huili Yang, Hongling Xu, Meirong Qin, Ping Wang, Jiangyong Gu, Yufeng Xing:
Identification of Potential TMPRSS2 Inhibitors for COVID-19 Treatment in Chinese Medicine by Computational Approaches and Surface Plasmon Resonance Technology. 3005-3017 - Lijun Lang, Antonio Frontera, Alberto Perez, Antonio Bauzá:
Computational Study of Driving Forces in ATSP, PDIQ, and P53 Peptide Binding: C═O···C═O Tetrel Bonding Interactions at Work. 3018-3029 - Karoline Sanches, Viktor Prypoten, K. George Chandy, David K. Chalmers, Raymond S. Norton:
Interaction of the Inhibitory Peptides ShK and HmK with the Voltage-Gated Potassium Channel KV1.3: Role of Conformational Dynamics. 3043-3053 - Amrutha Keshavamurthy, Prasanna D. Revanasiddappa, Sneha M. Dixit, Gandasi R. Priyanka:
Bound Phospholipids Assist Cholesteryl Ester Transfer in the Cholesteryl Ester Transfer Protein. 3054-3067 - Evan J. van Aalst, Corey J. McDonald, Benjamin J. Wylie:
Cholesterol Biases the Conformational Landscape of the Chemokine Receptor CCR3: A MAS SSNMR-Filtered Molecular Dynamics Study. 3068-3085 - Riccardo Rozza, Pavel Janos, Alessandra Magistrato:
Monovalent Ionic Atmosphere Modulates the Selection of Suboptimal RNA Sequences by Splicing Factors' RNA Recognition Motifs. 3086-3093 - Almotasem Belah Alhamwi, Canan Atilgan, Özge Sensoy:
Nonlocal Effects of Antibiotic-Resistance-Causing Mutations Reveal an Alternative Region for Targeting on FtsW-Penicillin-Binding Protein 3 Complex of Haemophilus influenzae. 3094-3104 - Jon Uranga, Ricardo A. Mata:
The Catalytic Mechanism of Acetoacetate Decarboxylase: A Detailed Study of Schiff Base Formation, Protonation States, and Their Impact on Catalysis. 3118-3127 - Joel Graef, Christiane Ehrt, Matthias Rarey:
Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3. 3128-3137 - Lucija Hok, Robert Vianello:
Selective Deuteration Improves the Affinity of Adenosine A2A Receptor Ligands: A Computational Case Study with Istradefylline and Caffeine. 3138-3149 - Rameshwar L. Kumawat, C. David Sherrill:
High-Order Quantum-Mechanical Analysis of Hydrogen Bonding in Hachimoji and Natural DNA Base Pairs. 3150-3157 - Erik Endres, Natalia Yuan Chen, Christoph A. Sotriffer:
MD-Based Assessment of Covalent Inhibitors in Noncovalent Association Complexes: Learning from Cathepsin K as a Test Case. 3186-3197 - Robert Fraczkiewicz, Marvin Waldman:
pK50─A Rigorous Indicator of Individual Functional Group Acidity/Basicity in Multiprotic Compounds. 3198-3208 - Javier Vázquez, Tiziana Ginex, Albert Herrero, Christophe Morisseau, Bruce D. Hammock, F. Javier Luque:
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits. 3209-3225
Volume 63, Number 11, June 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Thereza A. Soares, Zoe Cournia, Kevin J. Naidoo, Rommie E. Amaro, Habibah A. Wahab, Kenneth M. Merz Jr.:
Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. 3227-3229 - Yong Xiao Yang, Jin Yan Huang, Pan Wang, Bao Ting Zhu:
AREA-AFFINITY: A Web Server for Machine Learning-Based Prediction of Protein-Protein and Antibody-Protein Antigen Binding Affinities. 3230-3237 - Tobiasz Cieplinski, Tomasz Danel, Sabina Podlewska, Stanislaw Jastrzebski:
Generative Models Should at Least Be Able to Design Molecules That Dock Well: A New Benchmark. 3238-3247 - Shayma El-Atawneh, Amiram Goldblum:
Activity Models of Key GPCR Families in the Central Nervous System: A Tool for Many Purposes. 3248-3262 - Cheng Fang, Ye Wang, Richard Grater, Sudarshan Kapadnis, Cheryl Black, Patrick E. Trapa, Simone Sciabola:
Prospective Validation of Machine Learning Algorithms for Absorption, Distribution, Metabolism, and Excretion Prediction: An Industrial Perspective. 3263-3274 - Hossein Hajiabolhassan, Zahra Taheri, Ali Hojatnia, Yavar Taheri Yeganeh:
FunQG: Molecular Representation Learning via Quotient Graphs. 3275-3287 - Yiwen Lu, Dilek Yalcin, Paul J. Pigram, Lewis D. Blackman, Mario Boley:
Interpretable Machine Learning Models for Phase Prediction in Polymerization-Induced Self-Assembly. 3288-3306 - Po-Yu Kao, Ya-Chu Yang, Wei-Yin Chiang, Jen-Yueh Hsiao, Yudong Cao, Alex Aliper, Feng Ren, Alán Aspuru-Guzik, Alex Zhavoronkov, Min-Hsiu Hsieh, Yen-Chu Lin:
Exploring the Advantages of Quantum Generative Adversarial Networks in Generative Chemistry. 3307-3318 - Jike Wang, Yundian Zeng, Huiyong Sun, Junmei Wang, Xiaorui Wang, Ruofan Jin, Mingyang Wang, Xujun Zhang, Dong-Sheng Cao, Xi Chen, Chang-Yu Hsieh, Tingjun Hou:
Molecular Generation with Reduced Labeling through Constraint Architecture. 3319-3327 - Arun K. Rathod, Dhruvil Chavda, Moutusi Manna:
Phase Transition and Phase Separation in Realistic Thylakoid Lipid Membrane of Marine Algae in All-Atom Simulations. 3328-3339 - Mario Öeren, Sylvia C. Kaempf, David J. Ponting, Peter A. Hunt, Matthew D. Segall:
Predicting Regioselectivity of Cytosolic Sulfotransferase Metabolism for Drugs. 3340-3349 - Xu Qian, Xiaowen Dai, Lin Luo, Mingde Lin, Yuan Xu, Yang Zhao, Dingfang Huang, Haodi Qiu, Li Liang, Haichun Liu, Yingbo Liu, Lingxi Gu, Tao Lu, Yadong Chen, Yanmin Zhang:
An Interpretable Multitask Framework BiLAT Enables Accurate Prediction of Cyclin-Dependent Protein Kinase Inhibitors. 3350-3368 - Shinji Iida, Tomoshi Kameda:
Dissociation Rate Calculation via Constant-Force Steered Molecular Dynamics Simulation. 3369-3376 - Bharat Medasani, Sashank Kasiraju, Dionisios G. Vlachos:
OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions. 3377-3391 - Jan P. Unsleber:
Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application. 3392-3403 - Pabitra Narayan Samanta, Devashis Majumdar, Jerzy Leszczynski:
Elucidating Atomistic Insight into the Dynamical Responses of the SARS-CoV-2 Main Protease for the Binding of Remdesivir Analogues: Leveraging Molecular Mechanics To Decode the Inhibition Mechanism. 3404-3422 - Stephanie Wills, Ruben Sanchez-Garcia, Tim Dudgeon, Stephen D. Roughley, Andy Merritt, Roderick E. Hubbard, James Davidson, Frank von Delft, Charlotte M. Deane:
Fragment Merging Using a Graph Database Samples Different Catalogue Space than Similarity Search. 3423-3437 - Darren J. Hsu, Russell B. Davidson, Ada Sedova, Jens Glaser:
tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking. 3438-3447 - Bart M. H. Bruininks, Tsjerk A. Wassenaar, Ilpo Vattulainen:
Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries. 3448-3452 - Adekunle Aina, Shawn C. C. Hsueh, Steven S. Plotkin:
PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles. 3453-3461 - Eric R. Hantz, Svetlana B. Tikunova, Natalya Belevych, Jonathan P. Davis, Peter J. Reiser, Steffen Lindert:
Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscles and Structure-Activity Relationship. 3462-3473 - Bin Sun, Te Liu, Manjie Zhang, Shuijie Li:
Synergistic Binding of ATP and Nucleic Acids Necessitates UPF1's ATPase Functional Cycle. 3474-3485 - Martin Ljubic, Eva Prasnikar, Andrej Perdih, Jure Borisek:
All-Atom Simulations Reveal the Intricacies of Signal Transduction upon Binding of the HLA-E Ligand to the Transmembrane Inhibitory CD94/NKG2A Receptor. 3486-3499 - Niu Zhang, Zhicheng Zuo:
Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition. 3500-3509 - Felipe Curtolo, Guilherme Menegon Arantes:
Dissecting Reaction Mechanisms and Catalytic Contributions in Flavoprotein Fumarate Reductases. 3510-3520 - Joseph Clayton, Vinícius Martins de Oliveira, Mohamed Fouad Ibrahim, Xinyuanyuan Sun, Paween Mahinthichaichan, Mingzhe Shen, Rolf Hilgenfeld, Jana Shen:
Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease. 3521-3533 - Austin M. Cool, Steffen Lindert:
Umbrella Sampling Simulations of Cardiac Thin Filament Reveal Thermodynamic Consequences of Troponin I Inhibitory Peptide Mutations. 3534-3543 - Guillem Vila-Julià, Juan Jesús Pérez, Jaime Rubio-Martinez:
A Step Forward toward Selective Activation/Inhibition of Bak, a Pro-Apoptotic Member of the Bcl-2 Protein Family: Discovery of New Prospective Allosteric Sites Using Molecular Dynamics. 3544-3556 - Samuel Cajahuaringa, Daniel L. Z. Caetano, Leandro N. Zanotto, Guido Araujo, Munir S. Skaf:
MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies. 3557-3566 - Ying Wang, Jia Xu, Fengjuan Huang, Jiajia Yan, Xinjie Fan, Yu Zou, Chuang Wang, Feng Ding, Yunxiang Sun:
SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges. 3567-3578 - Fangying Li, Yujie Chen, Yiming Tang, Xianshi Liu, Guanghong Wei:
Dissecting the Effect of ALS Mutation G335D on the Early Aggregation of the TDP-43 Amyloidogenic Core Peptide: Helix-to-β-Sheet Transition and Conformational Shift. 3579-3590 - Fengjuan Huang, Ying Wang, Yu Zhang, Chuang Wang, Jiangfang Lian, Feng Ding, Yunxiang Sun:
Dissecting the Self-assembly Dynamics of Imperfect Repeats in α-Synuclein. 3591-3600 - Francesca Alessandra Ambrosio, Giosuè Costa, Isabella Romeo, Francesca Esposito, Mohammad Alkhatib, Romina Salpini, Valentina Svicher, Angela Corona, Paolo Malune, Enzo Tramontano, Francesca Ceccherini-Silberstein, Stefano Alcaro, Anna Artese:
Targeting SARS-CoV-2 Main Protease: A Successful Story Guided by an In Silico Drug Repurposing Approach. 3601-3613 - Yadi Xu, Xiaoyu Guo, Dengjie Yan, Xihan Dang, Li Guo, Tao Jia, Qiantao Wang:
Molecular Dynamics Simulation-Driven Focused Virtual Screening and Experimental Validation of Inhibitors for MTDH-SND1 Protein-Protein Interaction. 3614-3627
Volume 63, Number 12, June 2023
- Martin Sícho, Sohvi Luukkonen, Helle W. van den Maagdenberg, Linde Schoenmaker, Olivier J. M. Béquignon, Gerard J. P. van Westen:
DrugEx: Deep Learning Models and Tools for Exploration of Drug-Like Chemical Space. 3629-3636 - Maria Bzówka, Weronika Bagrowska, Artur Góra:
Recent Advances in Studying Toll-like Receptors with the Use of Computational Methods. 3669-3687 - Dizhou Wu, Freddie R. Salsbury Jr.:
Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods. 3705-3718 - Jonas Elsborg, Arghya Bhowmik:
Equivariant Graph-Representation-Based Actor-Critic Reinforcement Learning for Nanoparticle Design. 3731-3741 - Yanfei Guan, Taegyo Lee, Ke Wang, Shu Yu, J. Christopher McWilliams:
SNAr Regioselectivity Predictions: Machine Learning Triggering DFT Reaction Modeling through Statistical Threshold. 3751-3760 - João Victor da Silva Guerra, Luiz F. G. Alves, Didier Bourissou, Paulo Sérgio Lopes-de-Oliveira, György Szalóki:
Cavity Characterization in Supramolecular Cages. 3772-3785 - Morgan Lawrenz, Mats Svensson, Mitsunori Kato, Karen H. Dingley, Jackson Chief Elk, Zhe Nie, Yefen Zou, Zachary Kaplan, H. Rachel Lagiakos, Hideyuki Igawa, Eric Therrien:
A Computational Physics-based Approach to Predict Unbound Brain-to-Plasma Partition Coefficient, Kp,uu. 3786-3798 - András F. Wacha, Zoltán Varga, Tamás Beke-Somfai:
Comparative Study of Molecular Mechanics Force Fields for β-Peptidic Foldamers: Folding and Self-Association. 3799-3813 - Charly Empereur-mot, Kasper B. Pedersen, Riccardo Capelli, Martina Crippa, Cristina Caruso, Mattia Perrone, Paulo Cesar Telles de Souza, Siewert J. Marrink, Giovanni M. Pavan:
Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG. 3827-3838 - Michael Souffrant, Xin-Qiu Yao, Donald Hamelberg:
Evolving Mutational Buildup in HIV-1 Protease Shifts Conformational Dynamics to Gain Drug Resistance. 3892-3902 - Yueying Yang, Yang Liu, Kuiru Sa, Hui Wang, Yu Lin, Hua Li, Lixia Chen:
Structure-Based Drug Design and Synthesis of Pyrrolidine-2,5-diones as Novel TNF-α Inhibitors. 3911-3924 - Ute F. Röhrig, Mathilde Goullieux, Marine Bugnon, Vincent Zoete:
Attracting Cavities 2.0: Improving the Flexibility and Robustness for Small-Molecule Docking. 3925-3940
Volume 63, Number 13, July 2023
- Salvatore Galati, Miriana Di Stefano, Marco Macchia, Giulio Poli, Tiziano Tuccinardi:
MolBook UNIPI─Create, Manage, Analyze, and Share Your Chemical Data for Free. 3977-3982 - Philippe Gendreau, Joseph-André Turk, Nicolas Drizard, Vinicius Barros Ribeiro da Silva, Clarisse Descamps, Yann Gaston-Mathé:
Molecular Assays Simulator to Unravel Predictors Hacking in Goal-Directed Molecular Generations. 3983-3998 - Nutaya Pravalphruekul, Maytus Piriyajitakonkij, Phond Phunchongharn, Supanida Piyayotai:
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder. 3999-4011 - Esther Heid, Charles McGill, Florence H. Vermeire, William H. Green Jr.:
Characterizing Uncertainty in Machine Learning for Chemistry. 4012-4029 - Yujie Qian, Jiang Guo, Zhengkai Tu, Connor W. Coley, Regina Barzilay:
RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing. 4030-4041 - Regina Pikalyova, Yuliana Zabolotna, Dragos Horvath, Gilles Marcou, Alexandre Varnek:
Chemical Library Space: Definition and DNA-Encoded Library Comparison Study Case. 4042-4055 - Juliana Castro-Amorim, Ana Oliveira, Ashis K. Mukherjee, Maria João Ramos, Pedro Alexandrino Fernandes:
Unraveling the Reaction Mechanism of Russell's Viper Venom Factor X Activator: A Paradigm for the Reactivity of Zinc Metalloproteinases? 4056-4069 - Serah W. Kimani, Julie Owen, Stuart R. Green, Fengling Li, Yanjun Li, Aiping Dong, Peter J. Brown, Suzanne Ackloo, David Kuter, Cindy Yang, Miranda Macaskill, Stephen Scott Mackinnon, Cheryl H. Arrowsmith, Matthieu Schapira, Vijay Shahani, Levon Halabelian:
Discovery of a Novel DCAF1 Ligand Using a Drug-Target Interaction Prediction Model: Generalizing Machine Learning to New Drug Targets. 4070-4078 - Eric Fagerberg, Marie Skepö:
Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining. 4079-4087 - Toshifumi Yui, Takuya Uto, Kotaro Noda:
Extended Ensemble Molecular Dynamics Study of Ammonia-Cellulose I Complex Crystal Models: Free-Energy Landscape and Atomistic Pictures of Ammonia Diffusion in the Crystalline Phase. 4088-4099 - Miguel Gallegos, Ángel Martín Pendás:
Developing a User-Friendly Code for the Fast Estimation of Well-Behaved Real-Space Partial Charges. 4100-4114 - Christine Y. Yeh, Jesus A. Izaguirre, Jack B. Greisman, Lindsay Willmore, Paul Maragakis, David E. Shaw:
A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. 4115-4124 - Mitchell Benton, Mercede Furr, Vivek Govind Kumar, Adithya Polasa, Feng Gao, Colin David Heyes, Thallapuranam K. Suresh Kumar, Mahmoud Moradi:
cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach. 4125-4137 - Débora Bublitz Anton, Júlia Galvez Bulhões Pedreira, Maria Luiza Zvirtes, Stefan Laufer, Rodrigo G. Ducati, Márcia Goettert, Luís Fernando S. M. Timmers:
Targeting SARS-CoV-2 Main Protease (MPro) with Kinase Inhibitors: A Promising Approach for Discovering Antiviral and Anti-inflammatory Molecules against SARS-CoV-2. 4138-4146 - Zhenhao Liu, Kuan Liang, Wenlang Liu, Tao Jiang, Rui Zhou, Mojie Duan, Zheng Zheng:
Molecular Insights on the Conformational Transitions and Activity Regulation of the c-Met Kinase Induced by Ligand Binding. 4147-4157 - Yanjun Feng, Changda Gong, Jieyu Zhu, Guixia Liu, Yun Tang, Weihua Li:
Prediction of Sites of Metabolism of CYP3A4 Substrates Utilizing Docking-Derived Geometric Features. 4158-4169 - Renqing Zeng, Longxue Cai, Jose Manuel Perez-Aguilar, Zonglin Gu, Xianfa Liu:
Robust Mechanical Destruction to the Cell Membrane of Carbon Nitride Polyaniline (C3N): A Molecular Dynamics Simulation Study. 4170-4179 - Sefora Naomi Agrò, Riccardo Rozza, Santiago Movilla, Jana Aupic, Alessandra Magistrato:
Molecular Dynamics Simulations Elucidate the Molecular Basis of Pre-mRNA Translocation by the Prp2 Spliceosomal Helicase. 4180-4189 - Yazdan Maghsoud, Chao Dong, G. Andrés Cisneros:
Investigation of the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol: A Computational Study. 4190-4206 - Song Li, Chao Hu, Song Ke, Chenxing Yang, Jun Chen, Yi Xiong, Hao Liu, Liang Hong:
LS-MolGen: Ligand-and-Structure Dual-Driven Deep Reinforcement Learning for Target-Specific Molecular Generation Improves Binding Affinity and Novelty. 4207-4215 - Jialin Bi, Junjie Wee, Xiang Liu, Cunquan Qu, Guanghui Wang, Kelin Xia:
Multiscale Topological Indices for the Quantitative Prediction of SARS CoV-2 Binding Affinity Change upon Mutations. 4216-4227 - Meenakshi Verma, Laxmikant Trivedi, Prema G. Vasudev:
Correction to "Interaction Patterns of Pyrazolopyrimidines with Receptor Proteins". 4228
Volume 63, Number 14, July 2023
- Daniel R. Bryan, John L. Kulp Jr., Manoj K. Mahapatra, Richard L. Bryan, Usha Viswanathan, Micah N. Carlisle, Surim Kim, William D. Schutte, Kevaughn V. Clarke, Tony T. Doan, John L. Kulp III:
BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation. 4229-4236 - Valentina Sora, Matteo Tiberti, Ludovica Beltrame, Deniz Dogan, Shahriyar Mahdi Robbani, Joshua Rubin, Elena Papaleo:
PyInteraph2 and PyInKnife2 to Analyze Networks in Protein Structural Ensembles. 4237-4245 - András F. Wacha, Justin A. Lemkul:
charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS. 4246-4252 - Rocío Mercado, Steven M. Kearnes, Connor W. Coley:
Data Sharing in Chemistry: Lessons Learned and a Case for Mandating Structured Reaction Data. 4253-4265 - Stanley Lo, Martin Seifrid, Théophile Gaudin, Alán Aspuru-Guzik:
Augmenting Polymer Datasets by Iterative Rearrangement. 4266-4276 - Xiaowei Shen, Shiding Zhang, Jianyu Long, Changjing Chen, Meng Wang, Ziheng Cui, Biqiang Chen, Tianwei Tan:
A Highly Sensitive Model Based on Graph Neural Networks for Enzyme Key Catalytic Residue Prediction. 4277-4290 - Keshavan Seshadri, Marimuthu Krishnan:
Molecular Dynamics and Machine Learning Study of Adrenaline Dynamics in the Binding Pocket of GPCR. 4291-4300 - Lulu Zheng, Bin Zhu, Zengrui Wu, Mei Guo, Jinyao Chen, Minghuang Hong, Guixia Liu, Weihua Li, Guobin Ren, Yun Tang:
Pharmaceutical Cocrystal Discovery via 3D-SMINBR: A New Network Recommendation Tool Augmented by 3D Molecular Conformations. 4301-4311 - Fabio Falcioni, Paul L. A. Popelier:
How to Compute Atomistic Insight in DFT Clusters: The REG-IQA Approach. 4312-4327 - Subhamoy Mahajan, Tian Tang:
Automated Parameterization of Coarse-Grained Polyethylenimine under a Martini Framework. 4328-4341 - Siddhant M. Lambor, Sashank Kasiraju, Dionisios G. Vlachos:
CKineticsDB─An Extensible and FAIR Data Management Framework and Datahub for Multiscale Modeling in Heterogeneous Catalysis. 4342-4354 - Yupeng Huang, Hong Zhang, Siyuan Jiang, Dajiong Yue, Xiaohan Lin, Jun Zhang, Yi Qin Gao:
DSDP: A Blind Docking Strategy Accelerated by GPUs. 4355-4363 - Ching Ching Lam, Jonathan M. Goodman:
CONFPASS: Fast DFT Re-Optimizations of Structures from Conformation Searches. 4364-4375 - Son Tung Ngo, Trung Hai Nguyen, Van V. Vu:
Morphology of a Transmembrane Aβ42 Tetramer via REMD Simulations. 4376-4382 - Ronen Zangi:
Multimerizations, Aggregation, and Transfer Reactions of Small Numbers of Molecules. 4383-4391 - Wei-Bo Cui, Xue Wei, Jing-Fu Guo, Xue-Li Hao, Lu-Yi Zou, Song Wang, Hui Li, Zhong-Min Su, Ai-Min Ren:
Molecular Design of Highly Efficient Heavy-Atom-free NpImidazole Derivatives for Two-Photon Photodynamic Therapy and ClO- Detection. 4392-4404 - Tareq Hameduh, Michal Mokry, Andrew D. Miller, Zbynek Heger, Yazan Haddad:
Solvent Accessibility Promotes Rotamer Errors during Protein Modeling with Major Side-Chain Prediction Programs. 4405-4422 - Meina Ren, Ziyi Ma, Lina Zhao, Yanjiao Wang, Hailong An, Fude Sun:
Self-Association of ACE-2 with Different RBD Amounts: A Dynamic Simulation Perspective on SARS-CoV-2 Infection. 4423-4432 - Tomás F. D. Silva, Hannah Visca, Craig Klumpp, Oleg A. Andreev, Yana K. Reshetnyak, Miguel Machuqueiro:
Arginine Residues Modulate the Membrane Interactions of pHLIP Peptides. 4433-4446 - Nuno F. B. Oliveira, Filipe E. P. Rodrigues, João N. M. Vitorino, Patrícia F. N. Faísca, Miguel Machuqueiro:
Interfacial Dynamics and Growth Modes of β2-Microglobulin Dimers. 4447-4457 - Shengzhe Deng, Haiwei Zhang, Rongpei Gou, Ding Luo, Zerong Liu, Feng Zhu, Weiwei Xue:
Structure-Based Discovery of a Novel Allosteric Inhibitor against Human Dopamine Transporter. 4458-4467 - Katsuki Takebe, Mamoru Suzuki, Takao Kuwada-Kusunose, Satoko Shirai, Kaori Fukuzawa, Tomoko Takamiya, Narikazu Uzawa, Hiroshi Iijima:
Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O-Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses. 4468-4476
Volume 63, Number 15, August 2023
- Emmanuel V. Péan, Matthew L. Davies:
PEARS: A Web Tool for Fitting Time-Resolved Photoluminescence Decays of Perovskite Materials. 4477-4482 - Trinidad Novoa, Rubén Laplaza, Francesca Peccati, Franck Fuster, Julia Contreras-García:
The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems. 4483-4489 - Jun Liao, Zirui Shu, Junyong Gao, Mincong Wu, Changjun Chen:
SurfPB: A GPU-Accelerated Electrostatic Calculation and Visualization Tool for Biomolecules. 4490-4496 - Jessica Lanini, Gianluca Santarossa, Finton Sirockin, Richard A. Lewis, Nikolas Fechner, Hubert Misztela, Sarah Lewis, Krzysztof Maziarz, Megan Stanley, Marwin H. S. Segler, Nikolaus Stiefl, Nadine Schneider:
PREFER: A New Predictive Modeling Framework for Molecular Discovery. 4497-4504 - Alexander Hagg, Karl N. Kirschner:
Open-Source Machine Learning in Computational Chemistry. 4505-4532 - Christophe Chipot:
Predictions from First-Principles of Membrane Permeability to Small Molecules: How Useful Are They in Practice? 4533-4544 - Tom Bailey, Adam Jackson, Razvan-Antonio Berbece, Kejun Wu, Nicole Hondow, Elaine B. Martin:
Gradient Boosted Machine Learning Model to Predict H2, CH4, and CO2 Uptake in Metal-Organic Frameworks Using Experimental Data. 4545-4551 - Takuto Koyama, Shigeyuki Matsumoto, Hiroaki Iwata, Ryosuke Kojima, Yasushi Okuno:
Improving Compound-Protein Interaction Prediction by Self-Training with Augmenting Negative Samples. 4552-4559 - Jin Da Tan, Balamurugan Ramalingam, Swee Liang Wong, Jayce Jian Wei Cheng, Yee-Fun Lim, Vijila Chellappan, Saif A. Khan, Jatin Kumar, Kedar Hippalgaonkar:
Transfer Learning of Full Molecular Weight Distributions via High-Throughput Computer-Controlled Polymerization. 4560-4573 - Sayandeep Biswas, Yunsie Chung, Josephine Ramirez, Haoyang Wu, William H. Green Jr.:
Predicting Critical Properties and Acentric Factors of Fluids Using Multitask Machine Learning. 4574-4588 - Jonathan Parkinson, Wei Wang:
Linear-Scaling Kernels for Protein Sequences and Small Molecules Outperform Deep Learning While Providing Uncertainty Quantitation and Improved Interpretability. 4589-4601 - Feyza Kelleci Çelik, Gül Karaduman:
Machine Learning-Based Prediction of Drug-Induced Hepatotoxicity: An OvA-QSTR Approach. 4602-4614 - Tianyi Wang, Ying Tan, Yu Zong Chen, Chunyan Tan:
Infrared Spectral Analysis for Prediction of Functional Groups Based on Feature-Aggregated Deep Learning. 4615-4622 - Daniel Platero-Rochart, Tatyana Krivobokova, Michael Gastegger, Gilbert Reibnegger, Pedro A. Sánchez-Murcia:
Prediction of Enzyme Catalysis by Computing Reaction Energy Barriers via Steered QM/MM Molecular Dynamics Simulations and Machine Learning. 4623-4632 - Yan Xiang, Yu-Hang Tang, Guang Lin, Daniel Reker:
Interpretable Molecular Property Predictions Using Marginalized Graph Kernels. 4633-4640 - William K. Weigel, Alba L. Montoya, Raphael M. Franzini:
Evaluation of the Topology Space of DNA-Encoded Libraries. 4641-4653 - Jokent T. Gaza, Ricky B. Nellas:
Reparameterization of Non-Bonded Parameters for Copper Ions in Plastocyanin: An Adaptive Force Matching Study. 4654-4663 - Mariano Spivak, John E. Stone, João Ribeiro, Jan Saam, Peter L. Freddolino, Rafael C. Bernardi, Emad Tajkhorshid:
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. 4664-4678 - Bo-Wen Yin, Jie-Lei Wang, Pu-Jie Xue, Teng-Shuo Zhang, Bin-Bin Xie, Lin Shen, Wei-Hai Fang:
Understanding the Excited-State Relaxation Mechanisms of Xanthophyll Lutein by Multi-configurational Electronic Structure Calculations. 4679-4690 - Lucas G. Viviani, Daria B. Kokh, Rebecca C. Wade, Antonia T. do Amaral:
Molecular Dynamics Simulations of the Human Ecto-5′-Nucleotidase (h-ecto-5′-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics. 4691-4707 - Xin Wang, Jing Ma, Jianhua Fan, Hui Zhu, Xingman Liu, Hongqiang Xia, Yingtao Liu:
Characterization of Type I/II g-C3N4/MoS2 van der Waals Heterostructures: A New Theoretical Insight. 4708-4715 - Petr Stadlbauer, Vojtech Mlýnský, Miroslav Krepl, Jirí Sponer:
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations. 4716-4731 - Samo Lesnik, Urban Bren, Tatiana Domratcheva, Ana-Nicoleta Bondar:
Fentanyl and the Fluorinated Fentanyl Derivative NFEPP Elicit Distinct Hydrogen-Bond Dynamics of the Opioid Receptor. 4732-4748 - Yan Li, Zhe Zhang, Renxiao Wang:
HydraMap v.2: Prediction of Hydration Sites and Desolvation Energy with Refined Statistical Potentials. 4749-4761 - Xue Zhang, Lei Li, Qingchuan Zheng:
Dissecting the Effect of Temperature on Hyperthermophilic Pf2001 Esterase Dimerization by Molecular Dynamics. 4762-4771 - Hugo Guterres, Wonpil Im:
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes. 4772-4779 - Haiyan Cai, Yingying Wang, Jing Zhang, Zhenquan Wei, Teng Yan, Chenxi Feng, Zhijian Xu, Aiwu Zhou, Yingli Wu:
Discovery of Novel SIRT1/2 Inhibitors with Effective Cytotoxicity against Human Leukemia Cells. 4780-4790 - Christopher Lockhart, Xingyu Luo, Audrey Olson, Bryan M. Delfing, Xavier E. Laracuente, Kenneth W. Foreman, Mikell Paige, Kylene Kehn-Hall, Dmitri K. Klimov:
Can Free Energy Perturbation Simulations Coupled with Replica-Exchange Molecular Dynamics Study Ligands with Distributed Binding Sites? 4791-4802 - Defa Huang, Cong Guo:
E46K Mutation of α-Synuclein Preorganizes the Intramolecular Interactions Crucial for Aggregation. 4803-4813 - Sarmistha Majumdar, Francesco Di Palma, Francesca Spyrakis, Sergio Decherchi, Andrea Cavalli:
Molecular Dynamics and Machine Learning Give Insights on the Flexibility-Activity Relationships in Tyrosine Kinome. 4814-4826 - Wijitra Meelua, Tanchanok Wanjai, Natechanok Thinkumrob, Ran Friedman, Jitrayut Jitonnom:
Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1-OH···Nucleophile in Transition State Stabilization in Arabidopsis thaliana Cell-Wall Invertase 1. 4827-4838 - Ebru Cetin, Tandac F. Guclu, Isik Kantarcioglu, Ilona K. Gaszek, Erdal Toprak, Ali Rana Atilgan, Burcu Dedeoglu, Canan Atilgan:
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR. 4839-4849 - Jiaqi Liu, Jian Wan, Yanliang Ren, Xubo Shao, Xin Xu, Li Rao:
DOX_BDW: Incorporating Solvation and Desolvation Effects of Cavity Water into Nonfitting Protein-Ligand Binding Affinity Prediction. 4850-4863 - Amit Kumar, Harish Vashisth:
Mechanism of Ligand Discrimination by the NMT1 Riboswitch. 4864-4874 - Deborah Palazzotti, Tommaso Felicetti, Stefano Sabatini, Stefano Moro, Maria Letizia Barreca, Mattia Sturlese, Andrea Astolfi:
Fighting Antimicrobial Resistance: Insights on How the Staphylococcus aureus NorA Efflux Pump Recognizes 2-Phenylquinoline Inhibitors by Supervised Molecular Dynamics (SuMD) and Molecular Docking Simulations. 4875-4887 - Flavio Costa, Riccardo Ocello, Carlo Guardiani, Alberto Giacomello, Matteo Masetti:
Integrated Approach Including Docking, MD Simulations, and Network Analysis Highlights the Action Mechanism of the Cardiac hERG Activator RPR260243. 4888-4899 - Christian Wennberg, Magnus Lundborg, Erik Lindahl, Lars Norlén:
Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics Simulations. 4900-4911 - Ruibin Liu, Erik Antonio Vázquez-Montelongo, Shuhua Ma, Jana Shen:
Quantum Descriptors for Predicting and Understanding the Structure-Activity Relationships of Michael Acceptor Warheads. 4912-4923 - Silvia Gervasoni, Isilay Öztürk, Camilla Guccione, Andrea Bosin, Paolo Ruggerone, Giuliano Malloci:
Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations. 4924-4933 - Shubham Vishnoi, Shayon Bhattacharya, Erica M. Walsh, Grace Ilevbare Okoh, Damien Thompson:
Computational Peptide Design Cotargeting Glucagon and Glucagon-like Peptide-1 Receptors. 4934-4947 - Xinyue Liu, Jinying Liu, Bangze Fu, Ruzhen Chen, Jianzhou Jiang, He Chen, Runa Li, Lin Xing, Liying Yuan, Xuetai Chen, Jing Zhang, Honglei Li, Shuzhen Guo, Feifei Guo, Jiachen Guo, Yuan Liu, Yaning Qi, Biyue Yu, Feng Xu, Dong Li, Zhongyang Liu:
DCABM-TCM: A Database of Constituents Absorbed into the Blood and Metabolites of Traditional Chinese Medicine. 4948-4959 - Xiao-Wei Liu, Tian-Yu Shi, Dong Gao, Cai-Yi Ma, Hao Lin, Dan Yan, Ke-Jun Deng:
iPADD: A Computational Tool for Predicting Potential Antidiabetic Drugs Using Machine Learning Algorithms. 4960-4969 - Ji Lv, Guixia Liu, Yuan Ju, Houhou Huang, Dalin Li, Ying Sun:
Identification of Robust Antibiotic Subgroups by Integrating Multi-Species Drug-Drug Interactions. 4970-4978
Volume 63, Number 16, August 2023
- Issue Editorial Masthead.
- Issue Publication Information.
- Henrique M. Cezar, Michele Cascella:
SANS Spectra with PLUMED: Implementation and Application to Metainference. 4979-4985 - Bing He, Zhuming Gong, Maxim Avdeev, Siqi Shi:
FFMDFPA: A FAIRification Framework for Materials Data with No-Code Flexible Semi-Structured Parser and Application Programming Interfaces. 4986-4994 - Susanta Das, Laleh Dinpazhoh, Kiyoto Aramis Tanemura, Kenneth M. Merz Jr.:
Rapid and Automated Ab Initio Metabolite Collisional Cross Section Prediction from SMILES Input. 4995-5000 - Kuo-Hao Lee, Jamie J. Manning, Jonathan A. Javitch, Lei Shi:
A Novel "Activation Switch" Motif Common to All Aminergic Receptors. 5001-5017 - Fan Zhang, Tao Zeng, Ruibo Wu:
QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis. 5018-5034 - Sherwin S. S. Ng, Yunpeng Lu:
Evaluating the Use of Graph Neural Networks and Transfer Learning for Oral Bioavailability Prediction. 5035-5044 - Johnathan von der Heyde, Walter Malone, Nusaiba Zaman, Abdelkader Kara:
Combining Deep Learning Neural Networks with Genetic Algorithms to Map Nanocluster Configuration Spaces with Quantum Accuracy at Low Computational Cost. 5045-5055 - Leslie Salas-Estrada, Davide Provasi, Xing Qiu, Husnu Ümit Kaniskan, Xi-Ping Huang, Jeffrey F. Diberto, João Marcelo Lamim Ribeiro, Jian Jin, Bryan L. Roth, Marta Filizola:
De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework. 5056-5065 - Sarveswara Rao Vangala, Sowmya Ramaswamy Krishnan, Navneet Bung, Rajgopal Srinivasan, Arijit Roy:
pBRICS: A Novel Fragmentation Method for Explainable Property Prediction of Drug-Like Small Molecules. 5066-5076 - Krittapong Deshsorn, Krittamate Payakkachon, Tanapat Chaisrithong, Kulpavee Jitapunkul, Luckhana Lawtrakul, Pawin Iamprasertkun:
Unlocking the Full Potential of Heteroatom-Doped Graphene-Based Supercapacitors through Stacking Models and SHAP-Guided Optimization. 5077-5088 - Jiacheng Ma, Zhenya Du, Zhanpeng Lei, Lewen Wang, Yinye Yu, Xin Ye, Wen Ou, Xingzhan Wei, Bin Ai, Yecheng Zhou:
Intermolecular 3D-MoRSE Descriptors for Fast and Accurate Prediction of Electronic Couplings in Organic Semiconductors. 5089-5096 - Yu Zhang, Jinhui Yu, Hongwei Song, Minghui Yang:
Structure-Based Reaction Descriptors for Predicting Rate Constants by Machine Learning: Application to Hydrogen Abstraction from Alkanes by CH3/H/O Radicals. 5097-5106 - Giuseppe Lamanna, Pietro Delre, Gilles Marcou, Michele Saviano, Alexandre Varnek, Dragos Horvath, Giuseppe Felice Mangiatordi:
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design. 5107-5119 - Chris Zhang, Mary Pitman, Anjali Dixit, Sumudu Leelananda, Henri Palacci, Meghan Lawler, Svetlana Belyanskaya, Lashadric Grady, Joe Franklin, Nicolas Tilmans, David L. Mobley:
Building Block-Based Binding Predictions for DNA-Encoded Libraries. 5120-5132 - Thomas Liphardt, Thomas Sander:
Fast Substructure Search in Combinatorial Library Spaces. 5133-5141 - Nara Lee Chon, Natalie Jean Schultz, Hongjin Zheng, Hai Lin:
Anion Pathways in the NarK Nitrate/Nitrite Exchanger. 5142-5152 - Matthew S. Johnson, Maciej Gierada, Eric D. Hermes, David H. Bross, Khachik Sargsyan, Habib N. Najm, Judit Zádor:
Pynta─An Automated Workflow for Calculation of Surface and Gas-Surface Kinetics. 5153-5168 - Wanlei Wei, Hervé Hogues, Traian Sulea:
Comparative Performance of High-Throughput Methods for Protein pKa Predictions. 5169-5181 - Shubhandra Tripathi, Nisanth N. Nair:
Temperature Accelerated Sliced Sampling to Probe Ligand Dissociation from Protein. 5182-5191 - Shubhashree Barik, Akarsh Kumar Dash, Moumita Saharay:
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations. 5192-5203 - Vid Ravnik, Marko Jukic, Urban Bren:
Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach. 5204-5219 - Florent Barbault, Éric Brémond, Julien Rey, Pierre Tufféry, François Maurel:
DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion. 5220-5231 - Haiyi Chen, Yue Guo, Shengqing Ye, Jintu Zhang, Haotian Zhang, Na Liu, Rui Zhou, Tingjun Hou, Hongguang Xia, Yu Kang, Mojie Duan:
On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate. 5232-5243 - Piyatida Pojtanadithee, Kowit Hengphasatporn, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, I. Putu Sukanadi, Warinthorn Chavasiri, Peter Wolschann, Thierry Langer, Yasuteru Shigeta, Phornphimon Maitarad, Kamonpan Sanachai, Thanyada Rungrotmongkol:
Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CLpro through Structure-Based Virtual Screening and Experimental Approaches. 5244-5258 - Federica Battistini, Alba Sala, Adam Hospital, Modesto Orozco:
Sequence-Dependent Properties of the RNA Duplex. 5259-5271 - Sian Xiao, Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady Verkhivker:
Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. 5272-5296 - Jianwen Zhang, Yalong Cong, Lili Duan, John Z. H. Zhang:
Combined Antibodies Evusheld against the SARS-CoV-2 Omicron Variants BA.1.1 and BA.5: Immune Escape Mechanism from Molecular Simulation. 5297-5308 - Mohammad Mehdi Ghahremanpour, Anastasia Saar, Julian Tirado-Rives, William L. Jorgensen:
Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease. 5309-5318 - Jeremy Lapierre, Jochen S. Hub:
Converging PMF Calculations of Antibiotic Permeation across an Outer Membrane Porin with Subkilocalorie per Mole Accuracy. 5319-5330 - Luz América Chi-Uluac, Somayeh Asgharpour, Rodolfo Guadalupe Blanco-Rodríguez, Marlet Martínez-Archundia:
Atomistic Molecular Insights into Angiotensin-(1-7) Interpeptide Interactions. 5331-5340 - Lin Wei, Min Xu, Zhiqiang Liu, Chongguo Jiang, Xiaohua Lin, Yaogang Hu, Xiaoming Wen, Rongfeng Zou, Chunwang Peng, Hongrui Lin, Guo Wang, Lijun Yang, Lei Fang, Mingjun Yang, Peiyu Zhang:
Hit Identification Driven by Combining Artificial Intelligence and Computational Chemistry Methods: A PI5P4K-β Case Study. 5341-5355 - Justin Carbone, Nicholas J. Paradis, Lucas Bennet, Mark C. Alesiani, Katherine R. Hausman, Chun Wu:
Inhibition Mechanism of Anti-TB Drug SQ109: Allosteric Inhibition of TMM Translocation of Mycobacterium Tuberculosis MmpL3 Transporter. 5356-5374 - Nitin Kumar Singh, Pratyasha Bhardwaj, Mithun Radhakrishna:
Hydrophobicity─A Single Parameter for the Accurate Prediction of Disordered Regions in Proteins. 5375-5383 - Meng-Meng Wei, Chang-Qing Yu, Li-Ping Li, Zhu-Hong You, Lei Wang:
BCMCMI: A Fusion Model for Predicting circRNA-miRNA Interactions Combining Semantic and Meta-path. 5384-5394
Volume 63, Number 17, September 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu:
Editorial: Harnessing the Power of Large Language Model-Based Chatbots for Scientific Discovery. 5395 - Mark A. Watson, Ryne C. Johnston, Art D. Bochevarov:
Comment on the Definition and Labeling of pK50. 5396-5399 - R. A. Talmazan, Maren Podewitz:
PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent. 5400-5407 - Barmak Mostofian, Holli-Joi Martin, Asghar Razavi, Shivam Patel, Bryce K. Allen, Woody Sherman, Jesus A. Izaguirre:
Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods. 5408-5432 - Olivier J. M. Béquignon, Jose C. Gómez-Tamayo, Eelke B. Lenselink, Steven Wink, Steven Hiemstra, Chi Chung Lam, Domenico Gadaleta, Alessandra Roncaglioni, Ulf Norinder, Bob van de Water, Manuel Pastor, Gerard J. P. van Westen:
Collaborative SAR Modeling and Prospective In Vitro Validation of Oxidative Stress Activation in Human HepG2 Cells. 5433-5445 - Luis Cesar de Azevedo, Ronaldo C. Prati:
Effect of Flattened Structures of Molecules and Materials on Machine Learning Model Training. 5446-5456 - Changchang Liu, Peter Kutchukian, Nhan D. Nguyen, Mohammed Alquraishi, Peter K. Sorger:
A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules. 5457-5472 - Han Zhang, Haoyuan Li, Hanshen Xin, Jianhua Zhang:
Property Prediction and Structural Feature Extraction of Polyimide Materials Based on Machine Learning. 5473-5483 - Mario Latendresse, Jeremiah P. Malerich, James Herson, Markus Krummenacker, Judy Szeto, Vi-Anh Vu, Nathan Collins, Peter B. Madrid:
SynRoute: A Retrosynthetic Planning Software. 5484-5495 - Loriano Storchi, Gabriele Cruciani, Simon Cross:
DeepGRID: Deep Learning Using GRID Descriptors for BBB Prediction. 5496-5512 - Moayad Alnammi, Shengchao Liu, Spencer S. Ericksen, Gene E. Ananiev, Andrew F. Voter, Song Guo, James L. Keck, F. Michael Hoffmann, Scott A. Wildman, Anthony Gitter:
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries. 5513-5528 - Srishyam Raghavan, Brian P. Chaplin, Shafigh Mehraeen:
Small-Molecule Adsorption Energy Predictions for High-Throughput Screening of Electrocatalysts. 5529-5538 - Mitsuru Ohno, Yoshihiro Hayashi, Qi Zhang, Yu Kaneko, Ryo Yoshida:
SMiPoly: Generation of a Synthesizable Polymer Virtual Library Using Rule-Based Polymerization Reactions. 5539-5548 - Thomas Seidel, Christian Permann, Oliver Wieder, Stefan M. Kohlbacher, Thierry Langer:
High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment. 5549-5570 - Regina Pikalyova, Yuliana Zabolotna, Dragos Horvath, Gilles Marcou, Alexandre Varnek:
Meta-GTM: Visualization and Analysis of the Chemical Library Space. 5571-5582 - Abhik Ghosh Moulick, Jaydeb Chakrabarti:
Fluctuation-Dominated Ligand Binding in Molten Globule Protein. 5583-5591 - Cesar de Oliveira, Karl Leswing, Shulu Feng, René Kanters, Robert Abel, Sathesh Bhat:
FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols Using Active Learning. 5592-5603 - Vladimír Sládek, Pavel Smak, Igor Tvaroska:
How E-, L-, and P-Selectins Bind to sLex and PSGL-1: A Quantification of Critical Residue Interactions. 5604-5618 - Ghazi Aljabal, Aik-Hong Teh, Beow Keat Yap:
In Silico Prediction and Biophysical Validation of Novel 14-3-3σ Homodimer Stabilizers. 5619-5630 - Giulia Bianco, Matthew Holcomb, Diogo Santos-Martins, Andreas F. Tillack, Althea T. Hansel-Harris, Stefano Forli:
Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species. 5631-5640 - Rafael Giordano Viegas, Murilo Nogueira Sanches, Alan A. Chen, Fernando V. Paulovich, Angel E. García, Vitor B. P. Leite:
Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop. 5641-5649 - Qianzhen Shao, Yaoyukun Jiang, Zhongyue J. Yang:
EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation. 5650-5659 - Shakuntala Dhurua, Madhurima Jana:
Sulfation Effects of Chondroitin Sulfate to Bind a Chemokine in Aqueous Medium: Conformational Heterogeneity and Dynamics from Molecular Simulation. 5660-5675 - Milorad Andjelkovic, Kirill Zinovjev, Carlos Alberto Ramos-Guzmán, Jose Javier Ruiz-Pernía, Iñaki Tuñón:
Elucidation of the Active Form and Reaction Mechanism in Human Asparaginase Type III Using Multiscale Simulations. 5676-5688 - Jun Hu, Yu-Xuan Tang, Yu Zhou, Zhe Li, Bing Rao, Gui-Jun Zhang:
Improving DNA 6mA Site Prediction via Integrating Bidirectional Long Short-Term Memory, Convolutional Neural Network, and Self-Attention Mechanism. 5689-5700
Volume 63, Number 18, September 2023
- Issue Editorial Masthead.
- Issue Publication Information.
- Raimondas Galvelis, Alejandro Varela-Rial, Stefan Doerr, Roberto Fino, Peter K. Eastman, Thomas E. Markland, John D. Chodera, Gianni De Fabritiis:
NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics. 5701-5708 - Susanne Sauer, Hans Matter, Gerhard Hessler, Christoph Grebner:
Integrating Reaction Schemes, Reagent Databases, and Virtual Libraries into Fragment-Based Design by Reinforcement Learning. 5709-5726 - Ryann Perez, Xinning Li, Sam Giannakoulias, E. James Petersson:
AggBERT: Best in Class Prediction of Hexapeptide Amyloidogenesis with a Semi-Supervised ProtBERT Model. 5727-5733 - Maho Nakata, Toshiyuki Maeda:
PubChemQC B3LYP/6-31G*//PM6 Data Set: The Electronic Structures of 86 Million Molecules Using B3LYP/6-31G* Calculations. 5734-5754 - Seunghee Han, Jaewan Lee, Sehui Han, Seyed Mohamad Moosavi, Jihan Kim, Changyoung Park:
Design of New Inorganic Crystals with the Desired Composition Using Deep Learning. 5755-5763 - Kohei Motojima, Abhijit Sen, Yoichi M. A. Yamada, Hiromasa Kaneko:
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions. 5764-5772 - Toni Sivula, Laxman Yetukuri, Tuomo Kalliokoski, Heikki Käsnänen, Antti Poso, Ina Pöhner:
Machine Learning-Boosted Docking Enables the Efficient Structure-Based Virtual Screening of Giga-Scale Enumerated Chemical Libraries. 5773-5783 - Nicholas B. Smith, Tim Jowett, Diana Yu, Elke Pahl, Anna L. Garden:
Comparison of Taboo Search Methods for Atomic Cluster Global Optimization with a Basin-Hopping Algorithm. 5784-5793 - Simon Axelrod, Eugene Shakhnovich, Rafael Gómez-Bombarelli:
Mapping the Space of Photoswitchable Ligands and Photodruggable Proteins with Computational Modeling. 5794-5802 - Guilherme Duarte Ramos Matos, Steven Pak, Robert C. Rizzo:
Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit. 5803-5822 - Suvankar Ghosh, Sunanda Chatterjee, Priyadarshi Satpati:
Effect of Spacer Length Modification of the Cationic Side Chain on the Energetics of Antimicrobial Peptide Binding to Membrane-Mimetic Bilayers. 5823-5833 - Daipayan Sarkar, Hyungro Lee, John W. Vant, Matteo Turilli, Josh Vincent Vermaas, Shantenu Jha, Abhishek Singharoy:
Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting. 5834-5846 - Zhixiang Wu, Zhongjie Han, Lianci Tao, Xiaohan Sun, Jingjie Su, Jianping Hu, Chunhua Li:
Dynamic Insights into the Self-Activation Pathway and Allosteric Regulation of the Orphan G-Protein-Coupled Receptor GPR52. 5847-5862 - Gangtong Huang, Huayuan Tang, Yuying Liu, Chi Zhang, Pu Chun Ke, Yunxiang Sun, Feng Ding:
Direct Observation of Seeded Conformational Conversion of hIAPP In Silico Reveals the Mechanisms for Morphological Dependence and Asymmetry of Fibril Growth. 5863-5873 - Irina D. Pogozheva, Stanislav Cherepanov, Sang-Jun Park, Malini Raghavan, Wonpil Im, Andrei L. Lomize:
Structural Modeling of Cytokine-Receptor-JAK2 Signaling Complexes Using AlphaFold Multimer. 5874-5895 - Zhiyuan Zhao, Jintong Du, Yu Du, Yuan Gao, Mingxuan Yu, Yingkai Zhang, Hao Fang, Xuben Hou:
Deciphering the Allosteric Activation Mechanism of SIRT6 Using Molecular Dynamics Simulations. 5896-5902 - Poonam Pandey, Alexander D. MacKerell Jr.:
Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules. 5903-5915 - Nicola Gambacorta, Fulvio Ciriaco, Nicola Amoroso, Cosimo Damiano Altomare, Jürgen Bajorath, Orazio Nicolotti:
CIRCE: Web-Based Platform for the Prediction of Cannabinoid Receptor Ligands Using Explainable Machine Learning. 5916-5926 - Claudia Llinas del Torrent, Iu Raïch, Angel Gonzalez, Nil Casajuana-Martin, Jaume Lillo, Joan Biel Rebassa, Carlos Ferreiro-Vera, Verónica Sánchez de Medina, Rafael Franco, Gemma Navarro, Leonardo Pardo:
The Leu/Val6.51 Side Chain of Cannabinoid Receptors Regulates the Binding Mode of the Alkyl Chain of Δ9-Tetrahydrocannabinol. 5927-5935 - Xiaowen Hu, Yihan Dong, Jiaxuan Zhang, Lei Deng:
HGCLMDA: Predicting mRNA-Drug Sensitivity Associations via Hypergraph Contrastive Learning. 5936-5946
Volume 63, Number 19, October 2023
- Ariane Nunes-Alves, Kenneth M. Merz Jr.:
AlphaFold2 in Molecular Discovery. 5947-5949 - Lawson T. Glasby, Rama Oktavian, Kewei Zhu, Joan L. Cordiner, Jason C. Cole, Peyman Z. Moghadam:
Augmented Reality for Enhanced Visualization of MOF Adsorbents. 5950-5955 - Yingchao Yan, Yang Zhao, Huifeng Yao, Jie Feng, Li Liang, Weijie Han, Xiaohe Xu, Chengtao Pu, Chengdong Zang, Lingfeng Chen, Yuanyuan Li, Haichun Liu, Tao Lu, Yadong Chen, Yanmin Zhang:
RPBP: Deep Retrosynthesis Reaction Prediction Based on Byproducts. 5956-5970 - Zhilong Liang, Zhenzhi Tan, Ruixin Hong, Wanli Ouyang, Jinying Yuan, Changshui Zhang:
Automatically Predicting Material Properties with Microscopic Images: Polymer Miscibility as an Example. 5971-5980 - Juhwan Noh, Hyunju Chang:
Data-Driven Prediction of Configurational Stability of Molecule-Adsorbed Heterogeneous Catalysts. 5981-5995 - Nicholas T. Runcie, Antonia S. J. S. Mey:
SILVR: Guided Diffusion for Molecule Generation. 5996-6005 - Daniel J. Hutton, Kari E. Cordes, Carine Michel, Florian Göltl:
Machine Learning-Based Prediction of Activation Energies for Chemical Reactions on Metal Surfaces. 6006-6013 - Marc Lehner, Paul Katzberger, Niels Maeder, Carl C. G. Schiebroek, Jakob Teetz, Gregory A. Landrum, Sereina Riniker:
DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment. 6014-6028 - Yingying Ma, Minjie Li, Yongkun Mu, Gang Wang, Wencong Lu:
Accelerated Design for High-Entropy Alloys Based on Machine Learning and Multiobjective Optimization. 6029-6042 - Kong Meng, Chenyu Huang, Yaxin Wang, Yunjiang Zhang, Shuyuan Li, Zhaolin Fang, Huimin Wang, Shihao Wei, Shaorui Sun:
BNM-CDGNN: Batch Normalization Multilayer Perceptron Crystal Distance Graph Neural Network for Excellent-Performance Crystal Property Prediction. 6043-6052 - Damian M. Wilary, Jacqueline M. Cole:
ReactionDataExtractor 2.0: A Deep Learning Approach for Data Extraction from Chemical Reaction Schemes. 6053-6067 - Kevin M. Lefrancois-Gagnon, Robert C. Mawhinney:
Toward Universal Substituent Constants: Relating QTAIM Functional Group Descriptors to Substituent Effect Proxies. 6068-6080 - Ali Hashemi, Sana Bougueroua, Marie-Pierre Gaigeot, Evgeny Pidko:
HiREX: High-Throughput Reactivity Exploration for Extended Databases of Transition-Metal Catalysts. 6081-6094 - Süleyman Selim Çinaroglu, Philip C. Biggin:
Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems. 6095-6108 - Diship Srivastava, Niladri Patra:
Telescoping-Solvation-Box Protocol-Based Umbrella Sampling Method for Potential Mean Force Estimation. 6109-6117 - Zhiyong Guo, Lei Wang, Deming Rao, Weiqiong Liu, Miaomiao Xue, Qisheng Fu, Mengwei Lu, Lingqia Su, Sheng Chen, Binju Wang, Jing Wu:
Conformational Switch of the 250s Loop Enables the Efficient Transglycosylation in GH Family 77. 6118-6128 - Tobias M. Prass, Patrick Garidel, Michaela Blech, Lars V. Schäfer:
Viscosity Prediction of High-Concentration Antibody Solutions with Atomistic Simulations. 6129-6140 - Eduardo R. Almeida, Priscila V. Z. Capriles Goliatt, Hélio F. Dos Santos, Fabien Picaud:
Translocation Processes of Pt(II)-Based Drugs through Human Breast Cancer Cell Membrane: In Silico Experiments. 6141-6155 - Ushashi Banerjee, Adithya Chedere, Raksha Padaki, Abhilash Mohan, Narmada Sambaturu, Amit Singh, Nagasuma Chandra:
PathTracer Comprehensively Identifies Hypoxia-Induced Dormancy Adaptations in Mycobacterium tuberculosis. 6156-6167
Volume 63, Number 20, October 2023
- Xiaodan Yin, Xiaorui Wang, Yuquan Li, Jike Wang, Yuwei Wang, Yafeng Deng, Tingjun Hou, Huanxiang Liu, Pei Luo, Xiaojun Yao:
CODD-Pred: A Web Server for Efficient Target Identification and Bioactivity Prediction of Small Molecules. 6169-6176 - Kornel Ozvoldik, Thomas Stockner, Elmar Krieger:
YASARA Model-Interactive Molecular Modeling from Two Dimensions to Virtual Realities. 6177-6182 - David A. Case, Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet Cagri Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R. Machado, Hai Minh Nguyen, Kurt A. O'Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason M. Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E. Cheatham, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.:
AmberTools. 6183-6191 - Rajesh K. Raju, Saurabh Sivakumar, Xiaoxiao Wang, Zachary W. Ulissi:
Cluster-MLP: An Active Learning Genetic Algorithm Framework for Accelerated Discovery of Global Minimum Configurations of Pure and Alloyed Nanoclusters. 6192-6197 - Thi Tuyet Van Tran, Hilal Tayara, Kil To Chong:
Recent Studies of Artificial Intelligence on In Silico Drug Absorption. 6198-6211 - Romain Botella, Andrey A. Kistanov, Wei Cao:
Swarm Smart Meta-Estimator for 2D/2D Heterostructure Design. 6212-6223 - Fathoni A. Musyaffa, Kirsten Rapp, Holger Gohlke:
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW. 6224-6238 - Ye Buehler, Jean-Louis Reymond:
Expanding Bioactive Fragment Space with the Generated Database GDB-13s. 6239-6248 - Shuyuan Li, Yunjiang Zhang, Zhaolin Fang, Kong Meng, Rui Tian, Hong He, Shaorui Sun:
Extracting the Synthetic Route of Pd-Based Catalysts in Methanol Steam Reforming from the Scientific Literature. 6249-6260 - Kushagra Kashyap, Pinaki Prasad Mahapatra, Shakil Ahmed, Erdem Buyukbingol, Mohammad Imran Siddiqi:
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening. 6261-6282 - Sergei F. Vyboishchikov:
Dense Neural Network for Calculating Solvation Free Energies from Electronegativity-Equalization Atomic Charges. 6283-6292 - Mark A. Hix, Alice R. Walker:
AutoParams: An Automated Web-Based Tool To Generate Force Field Parameters for Molecular Dynamics Simulations. 6293-6301 - Vincenzo Maria D'amore, Greta Donati, Elena Lenci, Beatrice Stefanie Ludwig, Susanne Kossatz, Monica Baiula, Andrea Trabocchi, Horst Kessler, Francesco Saverio Di Leva, Luciana Marinelli:
Molecular View on the iRGD Peptide Binding Mechanism: Implications for Integrin Activity and Selectivity Profiles. 6302-6315 - Zezheng Yang, Nana Zhou, Xukai Jiang, Lushan Wang:
Loop Evolutionary Patterns Shape Catalytic Efficiency of TRI101/201 for Trichothecenes: Insights into Protein-Substrate Interactions. 6316-6331 - Jacqueline C. Calderón, Passainte Ibrahim, Dorothea Gobbo, Francesco Luigi Gervasio, Timothy Clark:
Activation/Deactivation Free-Energy Profiles for the β2-Adrenergic Receptor: Ligand Modes of Action. 6332-6343 - Raphael V. R. Dias, Renan P. Pedro, Murilo Nogueira Sanches, Giovana C. Moreira, Vitor B. P. Leite, Icaro P. Caruso, Fernando A. de Melo, Leandro C. Oliveira:
Unveiling Metastable Ensembles of GRB2 and the Relevance of Interdomain Communication during Folding. 6344-6353 - João T. S. Coimbra, Pedro Alexandrino Fernandes, Maria João Ramos:
Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations. 6354-6365 - Hyeonjun Kim, Eunae Kim, Youngshang Pak:
Computational Probing of the Folding Mechanism of Human Telomeric G-Quadruplex DNA. 6366-6375 - Fengjuan Huang, Xinjie Fan, Ying Wang, Chuang Wang, Yu Zou, Jiangfang Lian, Feng Ding, Yunxiang Sun:
Unveiling Medin Folding and Dimerization Dynamics and Conformations via Atomistic Discrete Molecular Dynamics Simulations. 6376-6385 - M. Andrés Velasco-Saavedra, Efrén Mar-Antonio, Rodrigo Aguayo-Ortiz:
Molecular Insights into the Covalent Binding of Zoxamide to the β-Tubulin of Botrytis cinerea. 6386-6395 - Mark James Horgan, Lukas Zell, Bianka Siewert, Hermann Stuppner, Daniela Schuster, Veronika Temml:
Identification of Novel β-Tubulin Inhibitors Using a Combined In Silico/In Vitro Approach. 6396-6411 - Patricia Gómez-Gutiérrez, Jaime Rubio-Martinez, Juan Jesús Pérez:
Discovery of Hit Compounds Targeting the P4 Allosteric Site of K-RAS, Identified through Ensemble-Based Virtual Screening. 6412-6422 - Zhangyang Chen, Xingqing Xiao, Li Yang, Cheng Lian, Shouhong Xu, Honglai Liu:
Prion-like Aggregation of the Heptapeptide GNNQQNY into Amyloid Nanofiber Is Governed by Configuration Entropy. 6423-6435 - Yasaman Karami, Samuel Murail, Julien Giribaldi, Benjamin Lefranc, Florian Defontaine, Olivier Lesouhaitier, Jérôme Leprince, Sjoerd Jacob de Vries, Pierre Tufféry:
Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. 6436-6450 - Hai-Tao Zhu, Yuhao Xia, Gui-Jun Zhang:
E2EDA: Protein Domain Assembly Based on End-to-End Deep Learning. 6451-6461
Volume 63, Number 21, November 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Anton S. Kolodnitsky, Nikita Ionov, Anastasia V. Rudik, Dmitry Filimonov, Vladimir Poroikov:
HGMMX: Host Gut Microbiota Metabolism Xenobiotics Database. 6463-6468 - Marine Bugnon, Mathilde Goullieux, Ute F. Röhrig, Marta A. S. Perez, Antoine Daina, Olivier Michielin, Vincent Zoete:
SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization. 6469-6475 - Amandeep Singh Bhatia, Mandeep Kaur Saggi, Sabre Kais:
Quantum Machine Learning Predicting ADME-Tox Properties in Drug Discovery. 6476-6486 - Muhammad Yasir, Jinyoung Park, Eun-Taek Han, Won Sun Park, Jin-Hee Han, Yong-Soo Kwon, Hee-Jae Lee, Wanjoo Chun:
Machine Learning-Based Drug Repositioning of Novel Janus Kinase 2 Inhibitors Utilizing Molecular Docking and Molecular Dynamic Simulation. 6487-6500 - Lan Yu, Xiao He, Xiaomin Fang, Lihang Liu, Jinfeng Liu:
Deep Learning with Geometry-Enhanced Molecular Representation for Augmentation of Large-Scale Docking-Based Virtual Screening. 6501-6514 - Yan Xiang, Yu-Hang Tang, Zheng Gong, Hongyi Liu, Liang Wu, Guang Lin, Huai Sun:
Efficient Exploration of Chemical Compound Space Using Active Learning for Prediction of Thermodynamic Properties of Alkane Molecules. 6515-6524 - Zhe Wang, Haiyang Zhong, Jintu Zhang, Peichen Pan, Dong Wang, Huanxiang Liu, Xiaojun Yao, Tingjun Hou, Yu Kang:
Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets. 6525-6536 - Ali Raza, Jamal Uddin, Abdullah Almuhaimeed, Shahid Akbar, Quan Zou, Ashfaq Ahmad:
AIPs-SnTCN: Predicting Anti-Inflammatory Peptides Using fastText and Transformer Encoder-Based Hybrid Word Embedding with Self-Normalized Temporal Convolutional Networks. 6537-6554 - Nathan J. Rebello, Tzyy-Shyang Lin, Heeba Nazeer, Bradley D. Olsen:
BigSMARTS: A Topologically Aware Query Language and Substructure Search Algorithm for Polymer Chemical Structures. 6555-6568 - Laura Pascazio, Simon Rihm, Ali Naseri, Sebastian Mosbach, Jethro Akroyd, Markus Kraft:
Chemical Species Ontology for Data Integration and Knowledge Discovery. 6569-6586 - Uschi Dolfus, Hans Briem, Torben Gutermuth, Matthias Rarey:
Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead Structures. 6587-6597 - Andrew T. McNutt, Fatimah Bisiriyu, Sophia Song, Ananya Vyas, Geoffrey R. Hutchison, David Ryan Koes:
Conformer Generation for Structure-Based Drug Design: How Many and How Good? 6598-6607 - Fengyang Han, Dongxiao Hao, Xibing He, Luxuan Wang, Taoyu Niu, Junmei Wang:
Distribution of Bound Conformations in Conformational Ensembles for X-ray Ligands Predicted by the ANI-2X Machine Learning Potential. 6608-6618 - Kojiro Machi, Seiji Akiyama, Yuuya Nagata, Masaharu Yoshioka:
OSPAR: A Corpus for Extraction of Organic Synthesis Procedures with Argument Roles. 6619-6628 - Dmitry V. Zankov, Timur I. Madzhidov, Pavel G. Polishchuk, Pavel Sidorov, Alexandre Varnek:
Multi-Instance Learning Approach to the Modeling of Enantioselectivity of Conformationally Flexible Organic Catalysts. 6629-6641 - Mateo Barria-Urenda, Alvaro Ruiz-Fernandez, Carlos Gonzalez, Chris Oostenbrink, José Antonio Garate:
Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene. 6642-6654 - Garrett A. Stevenson, Dan Kirshner, Brian J. Bennion, Yue Yang, Xiaohua Zhang, Adam T. Zemla, Marisa W. Torres, Aidan Epstein, Derek Jones, Hyojin Kim, W. F. Drew Bennett, Sergio Ernesto Wong, Jonathan E. Allen, Felice C. Lightstone:
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method. 6655-6666 - Alessandro Nicoli, Verena Weber, Carlotta Bon, Alexandra Steuer, Stefano Gustincich, Raul R. Gainetdinov, Roman Lang, Stefano Espinoza, Antonella Di Pizio:
Structure-Based Discovery of Mouse Trace Amine-Associated Receptor 5 Antagonists. 6667-6680 - Faisal Ahmad, Nousheen Parvaiz, Alexander D. MacKerell Jr., Syed Sikander Azam:
Non-β Lactam Inhibitors of the Serine β-Lactamase blaCTX-M15 in Drug-Resistant Salmonella typhi. 6681-6695 - Icaro A. Simon, Evert J. Homan, Maikel Wijtmans, Michael Sundström, Rob Leurs, Iwan J. P. de Esch, Barbara Zarzycka:
PSW-Designer: An Open-Source Computational Platform for the Design and Virtual Screening of Photopharmacological Ligands. 6696-6705 - Leonard Dick, Barbara Kirchner:
CONAN─Novel Tool to Create and Analyze Liquids in Confined Space. 6706-6716 - Abd. Kakhar Umar, Patanachai K. Limpikirati, Jittima Amie Luckanagul:
From Linear to Nets: Multiconfiguration Polymer Structure Generation with PolyFlin. 6717-6726 - Wei-Hua Yang, Fang-Qi Yu, Rao Huang, Gui-Fang Shao, Tun-Dong Liu, Yu-Hua Wen:
Structural Determination and Hierarchical Evolution of Transition Metal Clusters Based on an Improved Self-Adaptive Differential Evolution with Neighborhood Search Algorithm. 6727-6739 - William Oliveira Soté, Aurélia Aparecida de Araújo Rodrigues, Moacyr Comar Junior:
In Silico Evaluation of Oligomeric Representations for Molecularly Imprinted Polymer Modeling Using a Biological Template. 6740-6755 - K. Michael Salerno, Janna Domenico, Nam Q. Le, Krithika Balakrishnan, Ryan J. McQuillen, Christopher D. Stiles, Ilia A. Solov'yov, Carlos F. Martino:
Long-Time Oxygen and Superoxide Localization in Arabidopsis thaliana Cryptochrome. 6756-6767 - Yinwei Gu, Yan Li, Baocai Ma, Ke Ren, Chen Cao, Ning Gu:
Probing Conformational Transition of TRPV5 Induced by Mechanical Force Using Coarse-Grained Molecular Dynamics. 6768-6777 - Jason Kurniawan, Takashi Ishida:
Comparing Supervised Learning and Rigorous Approach for Predicting Protein Stability upon Point Mutations in Difficult Targets. 6778-6788 - Samaneh Davoudi, Koen Raemdonck, Kevin Braeckmans, An Ghysels:
Capric Acid and Myristic Acid Permeability Enhancers in Curved Liposome Membranes. 6789-6806 - Jorge Enrique Hernández González, Alexandre Suman de Araujo:
Alchemical Calculation of Relative Free Energies for Charge-Changing Mutations at Protein-Protein Interfaces Considering Fixed and Variable Protonation States. 6807-6822 - Gilberto Pereira, Brian Jiménez-García, Riccardo Pellarin, Guillaume Launay, Sangwook Wu, Juliette Martin, Paulo Cesar Telles de Souza:
Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking. 6823-6833 - Yazdan Maghsoud, Vindi M. Jayasinghe-Arachchige, Pratibha Kumari, G. Andrés Cisneros, Jin Liu:
Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects. 6834-6850 - Marcelo Depólo Polêto, Justin A. Lemkul:
Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes. 6851-6862 - Lei Yu, Stephanie A. Barros, Chengzao Sun, Sandeep Somani:
Cyclic Peptide Linker Design and Optimization by Molecular Dynamics Simulations. 6863-6876 - Ezequiel N. Frigini, Rodolfo D. Porasso, Tamás Beke-Somfai, José Javier López Cascales, Ricardo D. Enriz, Sergio Pantano:
The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations. 6877-6889 - Raitis Bobrovs, Laura Drunka, Iveta Kanepe, Aigars Jirgensons, Amedeo Caflisch, Matteo Salvalaglio, Kristaps Jaudzems:
Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. 6890-6899 - Lorenzo Guidetti, Alfonso Zappia, Laura Scalvini, Francesca Romana Ferrari, Carmine Giorgio, Riccardo Castelli, Francesca Galvani, Federica Vacondio, Silvia Rivara, Marco Mor, Chiara Urbinati, Marco Rusnati, Massimiliano Tognolini, Alessio Lodola:
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity. 6900-6911 - Zixuan Cheng, Siaw San Hwang, Mrinal Bhave, Taufiq Rahman, Xavier Chee Wezen:
Combination of QSAR Modeling and Hybrid-Based Consensus Scoring to Identify Dual-Targeting Inhibitors of PLK1 and p38γ. 6912-6924 - Francini Fonseca Lopez, Jiayuan Miao, Jovan Damjanovic, Luca Bischof, Michael B. Braun, Yingjie Ling, Marcus D. Hartmann, Yu-Shan Lin, Joshua A. Kritzer:
Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders. 6925-6937 - Xiao Liu, Lei Zheng, Chu Qin, Yang Li, John Z. H. Zhang, Zhaoxi Sun:
Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host-Guest Systems. 6938-6946 - Shuai Wang, Hui Cui, Tiangang Zhang, Peiliang Wu, Toshiya Nakaguchi, Ping Xuan:
Graph Reasoning Method Based on Affinity Identification and Representation Decoupling for Predicting lncRNA-Disease Associations. 6947-6958
Volume 63, Number 22, November 2023
- Issue Editorial Masthead.
- Issue Publication Information.
- Shunzhou Wan, Agastya P. Bhati, Alexander D. Wade, Peter V. Coveney:
Ensemble-Based Approaches Ensure Reliability and Reproducibility. 6959-6963 - Valentin J. Hoerschinger, Franz Waibl, Nancy D. Pomarici, Johannes R. Loeffler, Charlotte M. Deane, Guy Georges, Hubert Kettenberger, Monica L. Fernández-Quintero, Klaus R. Liedl:
PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability. 6964-6971 - Shiru Wu, Xiaowei Yang, Xun Zhao, Zhipu Li, Min Lu, Xiaoji Xie, Jiaxu Yan:
Applications and Advances in Machine Learning Force Fields. 6972-6985 - Arsen Sultanov, Jean-Claude Crivello, Tabea Rebafka, Nataliya Sokolovska:
Data-Driven Score-Based Models for Generating Stable Structures with Adaptive Crystal Cells. 6986-6997 - Vidushi Sharma, Maxwell Giammona, Dmitry Zubarev, Andy Tek, Khanh Nugyuen, Linda Sundberg, Daniele Congiu, Young-Hye La:
Formulation Graphs for Mapping Structure-Composition of Battery Electrolytes to Device Performance. 6998-7010 - Yanling Wu, Kun Li, Menglong Li, Xuemei Pu, Yanzhi Guo:
Attention Mechanism-Based Graph Neural Network Model for Effective Activity Prediction of SARS-CoV-2 Main Protease Inhibitors: Application to Drug Repurposing as Potential COVID-19 Therapy. 7011-7031 - Tiago Janela, Jürgen Bajorath:
Anatomy of Potency Predictions Focusing on Structural Analogues with Increasing Potency Differences Including Activity Cliffs. 7032-7044 - Qingyang Dong, Jacqueline M. Cole:
Snowball 2.0: Generic Material Data Parser for ChemDataExtractor. 7045-7055 - Ahmad Aakash, Ramsha Kulsoom, Saba Khan, Musab Saeed Siddiqui, Deedar Nabi:
Novel Models for Accurate Estimation of Air-Blood Partitioning: Applications to Individual Compounds and Complex Mixtures of Neutral Organic Compounds. 7056-7066 - Mingyuan Xu, Hongming Chen:
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree. 7067-7082 - Manuel A. Llanos, Nicolas Enrique, Vega Esteban-López, Sebastian Scioli-Montoto, David Sánchez-Benito, María E. Ruiz, Verónica Milesi, Dolores E. López, Alan Talevi, Pedro Martín, Luciana Gavernet:
A Combined Ligand- and Structure-Based Virtual Screening To Identify Novel NaV1.2 Blockers: In Vitro Patch Clamp Validation and In Vivo Anticonvulsant Activity. 7083-7096 - Yuliang Shi, Dil K. Limbu, Zeyu Zhang, Mohammad R. Momeni, Farnaz A. Shakib:
Effects of Defects and Presence of Open-Metal Sites on the Structure and Dynamics of Water in Hydrophobic Zeolitic Imidazolate Frameworks. 7097-7106 - Xuechen Tang, Janik Kokot, Franz Waibl, Monica L. Fernández-Quintero, Anna S. Kamenik, Klaus R. Liedl:
Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity. 7107-7123 - Mirko Paulikat, GiovanniMaria Piccini, Emiliano Ippoliti, Giulia Rossetti, Fabio Arnesano, Paolo Carloni:
Physical Chemistry of Chloroquine Permeation through the Cell Membrane with Atomistic Detail. 7124-7132 - Candide Champion, René Gall, Benjamin Ries, Salomé Rieder, Emília P. Barros, Sereina Riniker:
Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases. 7133-7147 - Sebastian Schmitt, Gajanan Kanagalingam, Florian Fleckenstein, Daniel Froescher, Hans Hasse, Simon Stephan:
Extension of the MolMod Database to Transferable Force Fields. 7148-7158 - Mariah R. Pierce, Jingjing Ji, Sadie X. Novak, Michelle A. Sieburg, Shivangi Nangia, Shikha Nangia, James L. Hougland:
Combined Computational-Biochemical Approach Offers an Accelerated Path to Membrane Protein Solubilization. 7159-7170 - Manuela Maurer, Themis Lazaridis:
Transmembrane β-Barrel Models of α-Synuclein Oligomers. 7171-7179 - Brandon Havranek, Robel Demissie, Hyun Lee, Shuiyun Lan, Huanchun Zhang, Stefan G. Sarafianos, Anoklase Jean-Luc Ayitou, Shahidul M. Islam:
Discovery of Nirmatrelvir Resistance Mutations in SARS-CoV-2 3CLpro: A Computational-Experimental Approach. 7180-7188 - Rui Wang, Hongsong Feng, Guo-Wei Wei:
ChatGPT in Drug Discovery: A Case Study on Anticocaine Addiction Drug Development with Chatbots. 7189-7209 - Anastasia Saar, Mohammad Mehdi Ghahremanpour, Julian Tirado-Rives, William L. Jorgensen:
Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors. 7210-7218 - Furyal Ahmed, Charles L. Brooks III:
FASTDock: A Pipeline for Allosteric Drug Discovery. 7219-7227 - Lucia Cano-González, Johan D. Espinosa-Mendoza, Félix Matadamas-Martínez, Ariana Romero-Velásquez, Miguel Flores-Ramos, Luis Fernando Colorado-Pablo, Marco Antonio Cerbón-Cervantes, Rafael Castillo, Ignacio González-Sánchez, Lilián Yépez-Mulia, Alicia Hernández-Campos, Rodrigo Aguayo-Ortiz:
Structure-Based Optimization of Carbendazim-Derived Tubulin Polymerization Inhibitors through Alchemical Free Energy Calculations. 7228-7238 - Fang Ge, Muhammad Arif, Zihao Yan, Hanin H. Alahmadi, Apilak Worachartcheewan, Dong-Jun Yu, Watshara Shoombuatong:
MMPatho: Leveraging Multilevel Consensus and Evolutionary Information for Enhanced Missense Mutation Pathogenic Prediction. 7239-7257 - Jingxin Xie, Lijun Quan, Xuejiao Wang, Hongjie Wu, Zhi Jin, Deng Pan, Taoning Chen, Tingfang Wu, Qiang Lyu:
DeepMPSF: A Deep Learning Network for Predicting General Protein Phosphorylation Sites Based on Multiple Protein Sequence Features. 7258-7271
Volume 63, Number 23, December 2023
- Kevin J. Naidoo, Kenneth M. Merz Jr., Guo-Wei Wei:
Modeling Reactions from Chemical Theories to Machine Learning. 7273 - Kristine Degn, Ludovica Beltrame, Matteo Tiberti, Elena Papaleo:
PDBminer to Find and Annotate Protein Structures for Computational Analysis. 7274-7281 - Luís Queirós-Reis, João R. Mesquita, Andrea Brancale, Marcella Bassetto:
Exploring the Fatty Acid Binding Pocket in the SARS-CoV-2 Spike Protein - Confirmed and Potential Ligands. 7282-7298 - Melissa Marciesky, Diana S. Aga, Ian M. Bradley, Nirupam Aich, Carla Ng:
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS). 7299-7319 - Zhicheng Zhong, Zeying Li, Jie Yang, Qian Wang:
Unified Model to Predict gRNA Efficiency across Diverse Cell Lines and CRISPR-Cas9 Systems. 7320-7329 - Jackson W. Burns, David M. Rogers:
QuantumScents: Quantum-Mechanical Properties for 3.5k Olfactory Molecules. 7330-7337 - Mohammad Mehdi Ghahremanpour, Anastasia Saar, Julian Tirado-Rives, William L. Jorgensen:
Ensemble Geometric Deep Learning of Aqueous Solubility. 7338-7349 - Evan M. Askenazi, Emanuel A. Lazar, Ilya Grinberg:
Identification of High-Reliability Regions of Machine Learning Predictions Based on Materials Chemistry. 7350-7362 - Heqi Sun, Jianmin Wang, Hongyan Wu, Shenggeng Lin, Junwei Chen, Jinghua Wei, Shuai Lv, Yi Xiong, Dong-Qing Wei:
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions. 7363-7372 - Rui Li, Lin Chen, Xinheng He, Duanhua Cao, Zehong Zhang, Hualiang Jiang, Kaixian Chen, Xi Cheng:
Loops Mediate Agonist-Induced Activation of the Stimulator of Interferon Genes Protein. 7373-7381 - Robin Skånberg, Ingrid Hotz, Anders Ynnerman, Mathieu Linares:
VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics. 7382-7391 - Hiroaki Iwata, Taichi Nakai, Takuto Koyama, Shigeyuki Matsumoto, Ryosuke Kojima, Yasushi Okuno:
VGAE-MCTS: A New Molecular Generative Model Combining the Variational Graph Auto-Encoder and Monte Carlo Tree Search. 7392-7400 - Dakota L. Folmsbee, David Ryan Koes, Geoffrey R. Hutchison:
Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences. 7401-7411 - Shu-Sen Chen, Zack Meyer, Brendan Jensen, Alex Kraus, Allison C. Lambert, Daniel H. Ess:
ReaLigands: A Ligand Library Cultivated from Experiment and Intended for Molecular Computational Catalyst Design. 7412-7422 - Nuno M. S. Almeida, Semiha Kevser Bali, Deepak James, Cong Wang, Angela K. Wilson:
Binding of Per- and Polyfluoroalkyl Substances (PFAS) to the PPARγ/RXRα-DNA Complex. 7423-7443 - Rupesh Agarwal, Rajitha Rajeshwar T., Jeremy C. Smith:
Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking. 7444-7452 - Miroslava Nedyalkova, Giovanni Russo, Philip Loche, Marco Lattuada:
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics. 7453-7463 - Andreia Fortuna, Paulo J. Costa:
Assessment of Halogen Off-Center Point-Charge Models Using Explicit Solvent Simulations. 7464-7475 - Shitong Zhang, Yanjing He, Shengtang Liu, Zhengqing Zhang, Chongli Zhong:
Metal-Organic Framework Membrane Constructor: A Tool for High-Throughput Construction of Metal-Organic Framework Membrane Models. 7476-7486 - Xuan Fang, Vladimir Bogdanov, Jonathan P. Davis, Peter M. Kekenes-Huskey:
Molecular Insights into the MLCK Activation by CaM. 7487-7498 - Lihua Dong, Yongjun Liu:
Exploring the Substrate-Assisted Dehydration of Chorismate Catalyzed by Dehydratase MqnA from QM/MM Calculations: The Role of Pocket Residues and the Hydrolysis Mechanism of N17D Mutant. 7499-7507 - Riccardo Rozza, Pavel Janos, Alessandra Magistrato:
Assessing the Binding Mode of a Splicing Modulator Stimulating Pre-mRNA Binding to the Plastic U2AF2 Splicing Factor. 7508-7517 - Luise Jacobsen, Jonathan Hungerland, Vladimir Bacic, Luca Gerhards, Fabian Schuhmann, Ilia A. Solov'yov:
Introducing the Automated Ligand Searcher. 7518-7528 - Sutong Xiang, Zhe Wang, Rongfan Tang, Lingling Wang, Qinghua Wang, Yang Yu, Qirui Deng, Tingjun Hou, Haiping Hao, Huiyong Sun:
Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling. 7529-7544 - Sudarshan Behera, Sundaram Balasubramanian:
Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid. 7545-7556 - Minghua Zhao, Steven X. Xu, Yaning Yang, Min Yuan:
GGNpTCR: A Generative Graph Structure Neural Network for Predicting Immunogenic Peptides for T-cell Immune Response. 7557-7567 - Shide Liang, Chi Zhang, Mingfu Zhu:
Ab Initio Prediction of 3-D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling. 7568-7577 - Yuko Tsuchiya, Tomoki Yonezawa, Yu Yamamori, Hiroko Inoura, Masanori Osawa, Kazuyoshi Ikeda, Kentaro Tomii:
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins. 7578-7587 - Rupeng Dai, Xueting Bao, Ying Zhang, Yan Huang, Haohao Zhu, Kundi Yang, Bo Wang, Hongmei Wen, Wei Li, Jian Liu:
Hot-Spot Residue-Based Virtual Screening of Novel Selective Estrogen-Receptor Degraders for Breast Cancer Treatment. 7588-7602
Volume 63, Number 24, December 2023
- Issue Editorial Masthead.
- Issue Publication Information.
- Giulia Palermo, Thereza A. Soares:
Editorial: Editing DNA and RNA through Computations. 7603-7604 - Osvaldo N. Oliveira, Leonardo Christino, Maria Cristina Ferreira de Oliveira, Fernando Vieira Paulovich:
Artificial Intelligence Agents for Materials Sciences. 7605-7609 - Anthony T. Bogetti, Jeremy M. G. Leung, Lillian T. Chong:
LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways. 7610-7616 - Zhenxing Wu, Jihong Chen, Yitong Li, Yafeng Deng, Haitao Zhao, Chang-Yu Hsieh, Tingjun Hou:
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery. 7617-7627 - Yaguo Gong, Wei Ding, Panpan Wang, Qibiao Wu, Xiaojun Yao, Qingxia Yang:
Evaluating Machine Learning Methods of Analyzing Multiclass Metabolomics. 7628-7641 - Aaron G. Garrison, Javier Heras-Domingo, John R. Kitchin, Gabriel dos Passos Gomes, Zachary W. Ulissi, Samuel M. Blau:
Applying Large Graph Neural Networks to Predict Transition Metal Complex Energies Using the tmQM_wB97MV Data Set. 7642-7654 - Zhipeng Wu, Yejian Wu, Cheng Zhu, Xinyi Wu, Silong Zhai, Xinqiao Wang, Zhihao Su, Hongliang Duan:
Efficient Computational Framework for Target-Specific Active Peptide Discovery: A Case Study on IL-17C Targeting Cyclic Peptides. 7655-7668 - Di-Fan Liu, Yong-Xin Zhang, Wen-Zhuo Dong, Qi-Kun Feng, Shao-Long Zhong, Zhi-Min Dang:
High-Temperature Polymer Dielectrics Designed Using an Invertible Molecular Graph Generative Model. 7669-7675 - Ignacio Pérez-Correa, Pablo D. Giunta, Fernando J. Mariño, Javier A. Francesconi:
Transformer-Based Representation of Organic Molecules for Potential Modeling of Physicochemical Properties. 7676-7688 - Pei Zhang, Logan T. Kearney, Debsindhu Bhowmik, Zachary R. Fox, Amit K. Naskar, John Gounley:
Transferring a Molecular Foundation Model for Polymer Property Predictions. 7689-7698 - Ruixuan Wang, Zhikang Liu, Jiahao Gong, Qingping Zhou, Xiaoqing Guan, Guangbo Ge:
An Uncertainty-Guided Deep Learning Method Facilitates Rapid Screening of CYP3A4 Inhibitors. 7699-7710 - Chen-Hsuan Huang, Shiang-Tai Lin:
MARS Plus: An Improved Molecular Design Tool for Complex Compounds Involving Ionic, Stereo, and Cis-Trans Isomeric Structures. 7711-7728 - Rubina, Syed Tarique Moin:
Attempting Well-Tempered Funnel Metadynamics Simulations for the Evaluation of the Binding Kinetics of Methionine Aminopeptidase-II Inhibitors. 7729-7743 - Jan Cz. Dobrowolski, Slawomir Ostrowski:
HOMA Index Establishes Similarity to a Reference Molecule. 7744-7754 - Runduo Liu, Wenchao Li, Yufen Yao, Yinuo Wu, Hai-Bin Luo, Zhe Li:
Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function. 7755-7767 - Genki Kudo, Keisuke Yanagisawa, Ryunosuke Yoshino, Takatsugu Hirokawa:
AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics. 7768-7777 - Anjana V. Mathath, Bratin Kumar Das, Debashree Chakraborty:
Designing Reaction Coordinate for Ion-Induced Pore-Assisted Mechanism of Halide Ions Permeation through Lipid Bilayer by Umbrella Sampling. 7778-7790 - Juan José Galano-Frutos, Francho Nerín-Fonz, Javier Sancho:
Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations. 7791-7806 - Aharon Gomez, Tobias J. Erb, Helmut Grubmüller, Esteban Vöhringer-Martinez:
Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO2 Fixation. 7807-7815 - Matthijs L. A. Hakkennes, Francesco Buda, Sylvestre Bonnet:
MetalDock: An Open Access Docking Tool for Easy and Reproducible Docking of Metal Complexes. 7816-7825 - Dongxiao Yue, Hajime Hirao:
Mechanism of Selective Aromatic Hydroxylation in the Metabolic Transformation of Paclitaxel Catalyzed by Human CYP3A4. 7826-7836 - Huaxin Zhou, Haohao Fu, Xueguang Shao, Wensheng Cai:
Binding Thermodynamics of Fourth-Generation EGFR Inhibitors Revealed by Absolute Binding Free Energy Calculations. 7837-7846 - Mathilde Goullieux, Vincent Zoete, Ute F. Röhrig:
Two-Step Covalent Docking with Attracting Cavities. 7847-7859 - Naoki Ogawa, Masateru Ohta, Mitsunori Ikeguchi:
Conformational Selectivity of ITK Inhibitors: Insights from Molecular Dynamics Simulations. 7860-7872 - Daniel Del Hoyo, Martin Salinas, Alba Lomas, Eugenia Ulzurrun, Nuria E. Campillo, Carlos Oscar Sorzano:
Scipion-Chem: An Open Platform for Virtual Drug Screening. 7873-7885 - Jiahui Guan, Lantian Yao, Chia-Ru Chung, Peilin Xie, Yilun Zhang, Junyang Deng, Ying-Chih Chiang, Tzong-Yi Lee:
Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning. 7886-7898
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