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Journal of Chemical Information and Modeling, Volume 61
Volume 61, Number 1, January 2021
- Issue Publication Information.
- Issue Editorial Masthead.
- Junyong Lai
, Xiangbin Li, Yanxing Wang
, Shiqiu Yin, Jielong Zhou, Zhenming Liu
:
AIScaffold: A Web-Based Tool for Scaffold Diversification Using Deep Learning. 1-6 - Maria Korshunova
, Boris Ginsburg, Alexander Tropsha
, Olexandr Isayev
:
OpenChem: A Deep Learning Toolkit for Computational Chemistry and Drug Design. 7-13 - Feng-Xu Wu
, Jing-Fang Yang, Long-Can Mei
, Fan Wang
, Ge-Fei Hao
, Guangfu Yang
:
PIIMS Server: A Web Server for Mutation Hotspot Scanning at the Protein-Protein Interface. 14-20 - Wenqiang Jia, Zhuo Yang
, Minjian Yang, Liang Cheng, Zengrong Lei, Xiaojian Wang
:
Machine Learning Enhanced Spectrum Recognition Based on Computer Vision (SRCV) for Intelligent NMR Data Extraction. 21-25 - Edgar López-López
, Jürgen Bajorath
, José L. Medina-Franco
:
Informatics for Chemistry, Biology, and Biomedical Sciences. 26-35 - Minsup Kim, Kichul Park, Wonsang Kim, Sangwon Jung, Art E. Cho
:
Target-Specific Drug Design Method Combining Deep Learning and Water Pharmacophore. 36-45 - Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen
:
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. 46-66 - Rafael Mamede, Bruno Simões de-Almeida, Mengyao Chen, Qing-You Zhang
, João Aires-de-Sousa
:
Machine Learning Classification of One-Chiral-Center Organic Molecules According to Optical Rotation. 67-75 - Aurelio Antelo-Collado, Ramón Carrasco-Velar, Nicolás García-Pedrajas, Gonzalo Cerruela García
:
Effective Feature Selection Method for Class-Imbalance Datasets Applied to Chemical Toxicity Prediction. 76-94 - Rainier Barrett
, Andrew D. White
:
Investigating Active Learning and Meta-Learning for Iterative Peptide Design. 95-105 - Abhishek Aggarwal
, Vinayak Vinayak, Saientan Bag, Chiranjib Bhattacharyya, Umesh V. Waghmare
, Prabal K. Maiti
:
Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model. 106-114 - Derek P. Metcalf
, Andy Jiang
, Steven A. Spronk
, Daniel L. Cheney, C. David Sherrill
:
Electron-Passing Neural Networks for Atomic Charge Prediction in Systems with Arbitrary Molecular Charge. 115-122 - Eunji Kim
, Dongseon Lee, Youngchun Kwon, Min Sik Park, Youn-Suk Choi
:
Valid, Plausible, and Diverse Retrosynthesis Using Tied Two-Way Transformers with Latent Variables. 123-133 - Joydeep Munshi, Wei Chen
, TeYu Chien
, Ganesh Balasubramanian
:
Transfer Learned Designer Polymers For Organic Solar Cells. 134-142 - Thomas Specht
, Kerstin Münnemann
, Hans Hasse, Fabian Jirasek
:
Automated Methods for Identification and Quantification of Structural Groups from Nuclear Magnetic Resonance Spectra Using Support Vector Classification. 143-155 - Michael R. Maser
, Alexander Y. Cui
, Serim Ryou, Travis J. DeLano
, Yisong Yue, Sarah E. Reisman
:
Multilabel Classification Models for the Prediction of Cross-Coupling Reaction Conditions. 156-166 - Robert Schmidt
, Florian Krull, Anna Lina Heinzke
, Matthias Rarey
:
Disconnected Maximum Common Substructures under Constraints. 167-178 - Yuliana Zabolotna
, Arkadii I. Lin
, Dragos Horvath
, Gilles Marcou
, Dmitriy M. Volochnyuk, Alexandre Varnek
:
Chemography: Searching for Hidden Treasures. 179-188 - Jeffrey L. Mendenhall, Benjamin P. Brown
, Sandeepkumar Kothiwale, Jens Meiler:
BCL: : Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database. 189-201 - Shweta Singh Chauhan
, Deepak Kumar Sachan, Ramakrishnan Parthasarathi
:
FOCUS-DB: An Online Comprehensive Database on Food Additive Safety. 202-210 - Ben Joseph R. Cuyacot
, Ivo Durník, Cina Foroutan-Nejad
, Radek Marek
:
Anatomy of Base Pairing in DNA by Interacting Quantum Atoms. 211-222 - Natalia Díaz
, Dimas Suárez
:
Understanding the Conformational Properties of Fluorinated Polypeptides: Molecular Modelling of Unguisin A. 223-237 - Louis Bellmann
, Patrick Penner
, Matthias Rarey
:
Topological Similarity Search in Large Combinatorial Fragment Spaces. 238-251 - Rong Yang, Zhenxing Chen, Fuda Xie
, Mingxiang Xie, Na Liu, Ziren Su, Jiangyong Gu
, Ruizhi Zhao:
(+/-)-Borneol Reverses Mitoxantrone Resistance against P-Glycoprotein. 252-262 - Flaviu S. Cipcigan
, Paul Smith
, Jason Crain
, Anders Hogner
, Leonardo De Maria
, Antonio Llinàs
, Ekaterina Ratkova
:
Membrane Permeability in Cyclic Peptides is Modulated by Core Conformations. 263-269 - Guglielmo Monaco
, Francesco Ferdinando Summa
, Riccardo Zanasi
:
Program Package for the Calculation of Origin-Independent Electron Current Density and Derived Magnetic Properties in Molecular Systems. 270-283 - Zhe Huai, Zhaoxi Shen, Zhaoxi Sun:
Binding Thermodynamics and Interaction Patterns of Inhibitor-Major Urinary Protein-I Binding from Extensive Free-Energy Calculations: Benchmarking AMBER Force Fields. 284-297 - Leena Aggarwal, Parbati Biswas
:
Hydration Thermodynamics of the N-Terminal FAD Mutants of Amyloid-β. 298-310 - José-Emilio Sánchez-Aparicio, Laura Tiessler-Sala
, Lorea Velasco-Carneros
, Lorena Roldán-Martín, Giuseppe Sciortino
, Jean-Didier Maréchal
:
BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization. 311-323 - Neda Ojaghlou, Justin Airas
, Lauren M. McRae
, Cooper A. Taylor, Bill R. Miller, Carol A. Parish
:
Understanding the Structure and Apo Dynamics of the Functionally Active JIP1 Fragment. 324-334 - Filipe M. Sousa, Luís M. P. Lima
, Clément Arnarez, Manuela M. Pereira
, Manuel N. Melo
:
Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies. 335-346 - Tandac F. Guclu
, Nazli Kocatug, Ali Rana Atilgan
, Canan Atilgan
:
N-Terminus of the Third PDZ Domain of PSD-95 Orchestrates Allosteric Communication for Selective Ligand Binding. 347-357 - Lovika Mittal
, Mitul Srivastava, Anita Kumari
, Rajiv K. Tonk
, Amit Awasthi, Shailendra Asthana
:
Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1. 358-384 - Anastasia G. Konshina
, Peter V. Dubovskii
, Roman G. Efremov:
Stepwise Insertion of Cobra Cardiotoxin CT2 into a Lipid Bilayer Occurs as an Interplay of Protein and Membrane "Dynamic Molecular Portraits". 385-399 - Shuhua Ma, Jack A. Henderson
, Jana Shen
:
Exploring the pH-Dependent Structure-Dynamics-Function Relationship of Human Renin. 400-407 - Martín Soñora
, Leandro Martínez
, Sergio Pantano
, Matías R. Machado
:
Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus. 408-422 - Subhomoi Borkotoky
, Debajit Dey
, Manidipa Banerjee
:
Computational Insight Into the Mechanism of SARS-CoV-2 Membrane Fusion. 423-431 - Karnesh Jain
, Othman Ghribi, Jerome Delhommelle
:
Folding Free-Energy Landscape of α-Synuclein (35-97) Via Replica Exchange Molecular Dynamics. 432-443 - Biswajit Gorai
, Anil Kumar Sahoo
, Anand Srivastava
, Narendra M. Dixit
, Prabal K. Maiti
:
Concerted Interactions between Multiple gp41 Trimers and the Target Cell Lipidome May Be Required for HIV-1 Entry. 444-454 - Krzysztof K. Bojarski
, Sergey A. Samsonov
:
Role of Oligosaccharide Chain Polarity in Protein-Glycosaminoglycan Interactions. 455-466 - Horacio Pérez Sánchez
, Helena den-Haan, Alfonso Pérez-Garrido
, Jorge Peña-García, Sandipan Chakraborty
, Ilkay Erdogan Orhan
, Fatma Sezer Senol Deniz
, José Manuel Villalgordo:
Combined Structure and Ligand-Based Design of Selective Acetylcholinesterase Inhibitors. 467-480 - Katherine J. Schultz
, Sean M. Colby, Vivian S. Lin
, Aaron T. Wright
, Ryan S. Renslow
:
Ligand- and Structure-Based Analysis of Deep Learning-Generated Potential α2a Adrenoceptor Agonists. 481-492 - Hanyu Gao
, Jean Pauphilet
, Thomas J. Struble
, Connor W. Coley
, Klavs F. Jensen
:
Direct Optimization across Computer-Generated Reaction Networks Balances Materials Use and Feasibility of Synthesis Plans for Molecule Libraries. 493-504 - Jun Hu
, Liang Rao, Yi-Heng Zhu, Gui-Jun Zhang, Dong-Jun Yu
:
TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features. 505-515 - Ju Zhang, Jialin Yu, Dan Lin, Xinyun Guo, Huan He, Shaoping Shi
:
DeepCLA: A Hybrid Deep Learning Approach for the Identification of Clathrin. 516-524 - Ruyu Dai, Wei Zhang, Wending Tang, Evelien Wynendaele, Qizhi Zhu, Yannan Bin, Bart De Spiegeleer
, Junfeng Xia
:
BBPpred: Sequence-Based Prediction of Blood-Brain Barrier Peptides with Feature Representation Learning and Logistic Regression. 525-534 - Hugo Guterres
, Sang-Jun Park
, Wei Jiang
, Wonpil Im
:
Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures. 535-546
Volume 61, Number 2, February 2021
- Issue Editorial Masthead.
- Issue Publication Information.
- Guo-Wei Wei
, Thereza A. Soares
, Habibah A. Wahab
, Renxiao Wang
:
Computational Chemistry in Asia. 547 - Daniel Mulnaes
, Filip Koenig
, Holger Gohlke
:
TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction. 548-553 - Timur Gimadiev, Ramil I. Nugmanov
, Dinar Batyrshin, Timur I. Madzhidov, Satoshi Maeda, Pavel Sidorov, Alexandre Varnek:
Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data. 554-559 - Benjamin Ries
, Stephanie M. Linker, David F. Hahn
, Gerhard König
, Sereina Riniker
:
Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations. 560-564 - Charles N. Lowe
, Antony J. Williams
:
Enabling High-Throughput Searches for Multiple Chemical Data Using the U.S.-EPA CompTox Chemicals Dashboard. 565-570 - Aamir Mehmood
, Aman Chandra Kaushik
, Qiankun Wang, Cheng-Dong Li, Dong-Qing Wei:
Bringing Structural Implications and Deep Learning-Based Drug Identification for KRAS Mutants. 571-586 - Kevin McLoughlin
, Claire G. Jeong, Thomas D. Sweitzer, Amanda J. Minnich, Margaret Tse, Brian J. Bennion, Jonathan E. Allen
, Stacie Calad-Thomson, Tom Rush, Jim Brase:
Machine Learning Models to Predict Inhibition of the Bile Salt Export Pump. 587-602 - Benjamin P. Brown
, Jeffrey L. Mendenhall, Alexander R. Geanes, Jens Meiler:
General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps. 603-620 - Sowmya Ramaswamy Krishnan
, Navneet Bung
, Gopalakrishnan Bulusu
, Arijit Roy
:
Accelerating De Novo Drug Design against Novel Proteins Using Deep Learning. 621-630 - Andrei Buin, Hung Yi Chiang, S. Andrew Gadsden
, Faraz A. Alderson:
Permutationally Invariant Deep Learning Approach to Molecular Fingerprinting with Application to Compound Mixtures. 631-640 - Haris Hasic
, Takashi Ishida
:
Single-Step Retrosynthesis Prediction Based on the Identification of Potential Disconnection Sites Using Molecular Substructure Fingerprints. 641-652 - Sankalp Jain
, Vishal B. Siramshetty
, Vinicius M. Alves
, Eugene N. Muratov
, Nicole C. Kleinstreuer
, Alexander Tropsha
, Marc C. Nicklaus
, Anton Simeonov, Alexey V. Zakharov
:
Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods. 653-663 - Janosch Menke
, Oliver Koch
:
Using Domain-Specific Fingerprints Generated Through Neural Networks to Enhance Ligand-Based Virtual Screening. 664-675 - Anju Sharma
, Rajnish Kumar
, Shabnam Ranjta
, Pritish Kumar Varadwaj
:
SMILES to Smell: Decoding the Structure-Odor Relationship of Chemical Compounds Using the Deep Neural Network Approach. 676-688 - Yashaswi Pathak, Sarvesh Mehta, U. Deva Priyakumar
:
Learning Atomic Interactions through Solvation Free Energy Prediction Using Graph Neural Networks. 689-698 - Reed M. Stein, Ying Yang, Trent E. Balius
, Matt J. O'Meara
, Jiankun Lyu
, Jennifer Young, Khanh G. Tang, Brian K. Shoichet
, John J. Irwin:
Property-Unmatched Decoys in Docking Benchmarks. 699-714 - Aida Shahraki
, Ali Isbilir
, Berna Dogan
, Martin J. Lohse
, Serdar Durdagi
, Necla Birgul-Iyison
:
Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents. 715-728 - Mahendra Awale
, Jérôme Hert
, Laura Guasch
, Sereina Riniker
, Christian Kramer:
The Playbooks of Medicinal Chemistry Design Moves. 729-742 - Lucian Chan
, Geoffrey R. Hutchison
, Garrett M. Morris
:
Understanding Ring Puckering in Small Molecules and Cyclic Peptides. 743-755 - Matevz Pesek, Andraz Juvan, Jure Jakos
, Janez Kosmrlj
, Matija Marolt, Martin Gazvoda
:
Database Independent Automated Structure Elucidation of Organic Molecules Based on IR, 1H NMR, 13C NMR, and MS Data. 756-763 - Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige, Rajeev Prabhakar
:
Degradation of a Main Plastic Pollutant Polyethylene Terephthalate by Two Distinct Proteases (Neprilysin and Cutinase-like Enzyme). 764-776 - Daisuke Takaya
, Chiduru Watanabe
, Shunpei Nagase, Kikuko Kamisaka
, Yoshio Okiyama
, Hirotomo Moriwaki
, Hitomi Yuki
, Tomohiro Sato
, Noriyuki Kurita
, Yoichiro Yagi
, Tatsuya Takagi
, Norihito Kawashita
, Kenichiro Takaba
, Tomonaga Ozawa, Midori Takimoto-Kamimura, Shigenori Tanaka
, Kaori Fukuzawa
, Teruki Honma
:
FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method. 777-794 - Erna K. Wieduwilt
, Jean-Charles Boisson, Giancarlo Terraneo
, Eric Hénon
, Alessandro Genoni
:
A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach. 795-809 - Steven W. Rick
, Gregory J. Schwing, Christopher M. Summa:
An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations. 810-818 - Ivo Kabelka, Radim Brozek, Robert Vácha
:
Selecting Collective Variables and Free-Energy Methods for Peptide Translocation across Membranes. 819-830 - Ya Gao
, Jumin Lee
, Iain Peter Shand Smith
, Hwayoung Lee
, Seonghoon Kim
, Yifei Qi
, Jeffery B. Klauda
, Göran Widmalm
, Syma Khalid
, Wonpil Im
:
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides. 831-839 - Vilde Bråten
, Øivind Wilhelmsen
, Sondre Kvalvåg Schnell
:
Chemical Potential Differences in the Macroscopic Limit from Fluctuations in Small Systems. 840-855 - Shiji Zhao
, Andrew J. Schaub
, Shiou-Chuan Tsai
, Ray Luo
:
Development of a Pantetheine Force Field Library for Molecular Modeling. 856-868 - Arkajyoti Sengupta
, Zhen Li
, Lin Frank Song
, Pengfei Li
, Kenneth M. Merz Jr.
:
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. 869-880 - Yuemei Li
, Rui Wang
, Yongmei Li
, Wei Zheng:
First-Principles Calculation of Photoelectric Property in Upconversion Materials through In3+ Doping. 881-890 - Maohua Yang
, Yegen Tang, Jingwei Weng
, Zhijun Liu, Wenning Wang
:
The Role of Calcium in Regulating the Conformational Dynamics of d-Galactose/d-Glucose-Binding Protein Revealed by Markov State Model Analysis. 891-900 - Davide Sala
, Andrea Giachetti
, Antonio Rosato
:
Insights into the Dynamics of the Human Zinc Transporter ZnT8 by MD Simulations. 901-912 - Javier Rodríguez-Salarichs, Mario García de Lacoba, Alicia Prieto
, María Jesús Martínez
, Jorge Barriuso
:
Versatile Lipases from the Candida rugosa-like Family: A Mechanistic Insight Using Computational Approaches. 913-920 - Weikang Gong
, Yang Liu, Yanpeng Zhao
, Shihao Wang, Zhongjie Han, Chunhua Li:
Equally Weighted Multiscale Elastic Network Model and Its Comparison with Traditional and Parameter-Free Models. 921-937 - Hanne S. Antila
, Tiago M. Ferreira
, Samuli Ollila
, Markus Miettinen
:
Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics. 938-949 - Dizhou Wu, Jiajie Xiao
, Freddie R. Salsbury Jr.
:
Light Chain Mutation Effects on the Dynamics of Thrombin. 950-965 - Yunxiang Sun
, Junchao Huang
, Xiangmei Duan
, Feng Ding
:
Direct Observation of β-Barrel Intermediates in the Self-Assembly of Toxic SOD128-38 and Absence in Nontoxic Glycine Mutants. 966-975 - Lucy Kate Ladefoged
, Birgit Schiøtt
, Natalya U. Fedosova
:
Beneficent and Maleficent Effects of Cations on Bufadienolide Binding to Na+, K+-ATPase. 976-986 - Mayk C. Ramos, Bruno A. C. Horta
:
Drug-Loading Capacity of PAMAM Dendrimers Encapsulating Quercetin Molecules: A Molecular Dynamics Study with the 2016H66 Force Field. 987-1000 - André Fischer
, Florian Häuptli, Markus A. Lill
, Martin Smiesko
:
Computational Assessment of Combination Therapy of Androgen Receptor-Targeting Compounds. 1001-1009 - André Fischer
, Gabriela Frehner, Markus A. Lill
, Martin Smiesko
:
Conformational Changes of Thyroid Receptors in Response to Antagonists. 1010-1019 - Anjela Manandhar
, Benjamin E. Blass
, Dennis J. Colussi, Imane Almi, Magid Abou-Gharbia
, Michael L. Klein, Khaled M. Elokely
:
Targeting SARS-CoV-2 M3CLpro by HCV NS3/4a Inhibitors: In Silico Modeling and In Vitro Screening. 1020-1032
Volume 61, Number 3, March 2021
- Issue Editorial Masthead.
- Issue Publication Information.
- Tesia M. Bobrowski
, Daniel Robert Korn, Eugene N. Muratov
, Alexander Tropsha
:
ZINC Express: A Virtual Assistant for Purchasing Compounds Annotated in the ZINC Database. 1033-1036 - Junxi Mu, Hao Liu
, Jian Zhang
, Ray Luo
, Hai-Feng Chen
:
Recent Force Field Strategies for Intrinsically Disordered Proteins. 1037-1047 - Yunhui Ge
, David F. Hahn, David L. Mobley
:
A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations. 1048-1052 - Cheng-Wei Ju
, Hanzhi Bai, Bo Li
, Rizhang Liu:
Machine Learning Enables Highly Accurate Predictions of Photophysical Properties of Organic Fluorescent Materials: Emission Wavelengths and Quantum Yields. 1053-1065 - Ziteng Liu
, Liqiang Lin, Qingqing Jia, Zheng Cheng, Yanyan Jiang, Yanwen Guo, Jing Ma
:
Transferable Multilevel Attention Neural Network for Accurate Prediction of Quantum Chemistry Properties via Multitask Learning. 1066-1082 - José Jiménez-Luna
, Miha Skalic, Nils Weskamp
, Gisbert Schneider:
Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment. 1083-1094 - Jianing Lu, Song Xia, Jieyu Lu, Yingkai Zhang
:
Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning. 1095-1104 - Mrityunjay Singh
, Mitul Srivastava, Sharad R. Wakode
, Shailendra Asthana
:
Elucidation of Structural Determinants Delineates the Residues Playing Key Roles in Differential Dynamics and Selective Inhibition of Sirt1-3. 1105-1124 - Johnatan Mucelini, Marcos G. Quiles
, Ronaldo C. Prati
, Juarez L. F. Da Silva
:
Correlation-Based Framework for Extraction of Insights from Quantum Chemistry Databases: Applications for Nanoclusters. 1125-1135 - Batuhan Yildirim
, Jacqueline M. Cole
:
Bayesian Particle Instance Segmentation for Electron Microscopy Image Quantification. 1136-1149 - Tzyy-Shyang Lin, Nathan J. Rebello
, Haley K. Beech
, Zi Wang
, Bassil El-Zaatari, David J. Lundberg, Jeremiah A. Johnson
, Julia A. Kalow
, Stephen L. Craig
, Bradley D. Olsen
:
PolyDAT: A Generic Data Schema for Polymer Characterization. 1150-1163 - Anastasios Gotzias
:
Binding Free Energy Calculations of Bilayer Graphenes Using Molecular Dynamics. 1164-1171 - Kohei Sasaki, Takefumi Yamashita
:
Modification and Validation of the DREIDING Force Field for Molecular Liquid Simulations (DREIDING-UT). 1172-1179 - Jiahui Tong, Suwen Zhao
:
Large-Scale Analysis of Bioactive Ligand Conformational Strain Energy by Ab Initio Calculation. 1180-1192 - Christoph Öhlknecht
, Sonja Katz
, Christina Kröß, Bernhard Sprenger
, Petra Engele
, Rainer Schneider, Chris Oostenbrink
:
Efficient In Silico Saturation Mutagenesis of a Member of the Caspase Protease Family. 1193-1203 - Evgeny Moerman
, David Furman
, David J. Wales
:
Development of ReaxFF Reactive Force Field for Aqueous Iron-Sulfur Clusters with Applications to Stability and Reactivity in Water. 1204-1214 - Maria G. Khrenova
, Anna M. Kulakova
, Alexander V. Nemukhin
:
Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase. 1215-1225 - Frederico Campos Freitas
, Paulo Henrique Borges Ferreira
, Denize Cristina Favaro
, Ronaldo Junio de Oliveira
:
Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides. 1226-1243 - Andrés Mejía
, Erich A. Müller
, Gustavo Chaparro
:
SGTPy: A Python Code for Calculating the Interfacial Properties of Fluids Based on the Square Gradient Theory Using the SAFT-VR Mie Equation of State. 1244-1250 - Adrián Ricarte
, James A. R. Dalton
, Jesús Giraldo
:
Structural Assessment of Agonist Efficacy in the μ-Opioid Receptor: Morphine and Fentanyl Elicit Different Activation Patterns. 1251-1274 - Sifan Lyu, Yunshuo Zhao, Xiao Zeng
, Xiaotong Chen, Qingqing Meng, Zhe Ding, Wenshan Zhao, Yuanming Qi, Yanfeng Gao
, Jiangfeng Du
:
Identification of Phelligridin-Based Compounds as Novel Human CD73 Inhibitors. 1275-1286 - Richard D. Smith, Heather A. Carlson
:
Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. 1287-1299 - Ruirui Liu
, Hong Lin Zhai
, Yajie Meng
, Min Zhu, Tao Wen, Nengzhi Jin:
Adsorption Behaviors of Typical Proteins on BP, GR, and C2N Surfaces. 1300-1306 - Masataka Yamauchi
, Hisashi Okumura
:
Dimerization of α-Synuclein Fragments Studied by Isothermal-Isobaric Replica-Permutation Molecular Dynamics Simulation. 1307-1321 - Harsh Bansia
, Pranjal Mahanta, Neela H. Yennawar
, Suryanarayanarao Ramakumar:
Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches. 1322-1333 - Luise Jacobsen
, Peter Husen
, Ilia A. Solov'yov
:
Inhibition Mechanism of Antimalarial Drugs Targeting the Cytochrome bc1 Complex. 1334-1345 - Prasanthi Medarametla
, Thales Kronenberger
, Tuomo Laitinen
, Antti Poso
:
Structural Characterization of LsrK as a Quorum Sensing Target and a Comparison between X-ray and Homology Models. 1346-1353 - Giulio Alberini, Fabio Benfenati
, Luca Maragliano
:
Structural Mechanism of ω-Currents in a Mutated Kv7.2 Voltage Sensor Domain from Molecular Dynamics Simulations. 1354-1367 - Nan Bai, Sven A. Miller, Grigorii V. Andrianov, Max Yates
, Palani Kirubakaran, John Karanicolas
:
Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta. 1368-1382 - Mohsen Asadbegi
, Amir Shamloo
:
Evaluating the Multifunctionality of a New Modulator of Zinc-Induced Aβ Aggregation Using a Novel Computational Approach. 1383-1401 - Andrew Prussia
, Spandan Chennamadhavuni
:
Biostructural Models for the Binding of Nucleoside Analogs to SARS-CoV-2 RNA-Dependent RNA Polymerase. 1402-1411 - Richard S. Hong, Alessandra Mattei, Ahmad Y. Sheikh
, Rajni Miglani Bhardwaj, Michael A. Bellucci, Keith F. McDaniel
, M. Olivia Pierce, Guangxu Sun, Sizhu Li, Lingle Wang
, Sayan Mondal, Jianguo Ji, Thomas B. Borchardt:
Novel Physics-Based Ensemble Modeling Approach That Utilizes 3D Molecular Conformation and Packing to Access Aqueous Thermodynamic Solubility: A Case Study of Orally Available Bromodomain and Extraterminal Domain Inhibitor Lead Optimization Series. 1412-1426 - Saravana G. Baskaran, Thayne P. Sharp, Kim A. Sharp
:
Computational Graphics Software for Interactive Docking and Visualization of Ligand-Protein Complementarity. 1427-1443 - Maria-Anna Trapotsi
, Lewis H. Mervin
, Avid M. Afzal, Noé Sturm, Ola Engkvist
, Ian P. Barrett, Andreas Bender
:
Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions. 1444-1456 - Yuliia Orlova
, Alessa A. Gambardella, Ivan Kryven
, Katrien Keune, Piet D. Iedema:
Generative Algorithm for Molecular Graphs Uncovers Products of Oil Oxidation. 1457-1469 - Ayush Jhunjhunwala, Zakir Ali
, Sohini Bhattacharya, Antarip Halder
, Abhijit Mitra
, Purshotam Sharma:
On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions. 1470-1480 - Barnali Das
, Pralay Mitra
:
High-Performance Whole-Cell Simulation Exploiting Modular Cell Biology Principles. 1481-1492 - Lucas S. P. Rudden
, Matteo T. Degiacomi
:
Transmembrane Protein Docking with JabberDock. 1493-1499 - Chao Li, Jun Sun
, Vasile Palade:
MSLDOCK: Multi-Swarm Optimization for Flexible Ligand Docking and Virtual Screening. 1500-1515 - Sergio A. Poveda-Cuevas
, Fernando Luís Barroso da Silva, Catherine Etchebest
:
How the Strain Origin of Zika Virus NS1 Protein Impacts Its Dynamics and Implications to Their Differential Virulence. 1516-1530
Volume 61, Number 4, April 2021
- Issue Editorial Masthead.
- Issue Publication Information.
- Matthias Rarey
, Marc C. Nicklaus
, Wendy A. Warr
:
Call for Papers for the Special Issue: From Reaction Informatics to Chemical Space. 1531-1532 - Johannes Kraml, Florian Hofer, Patrick K. Quoika
, Anna S. Kamenik
, Klaus R. Liedl
:
X-Entropy: A Parallelized Kernel Density Estimator with Automated Bandwidth Selection to Calculate Entropy. 1533-1538 - Mayk C. Ramos, Patrick K. Quoika
, Vitor A. C. Horta, Douglas Mota Dias, Elan G. Costa, Jorge Luís Machado do Amaral, Luigi M. Ribeiro, Klaus R. Liedl
, Bruno A. C. Horta
:
pyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules. 1539-1544 - Kexin Zhang, Kyrillos Abdallah
, Pujan Ajmera
, Kyle Finos, Andrew Looka
, Joseph Mekhael
, Aaron T. Frank
:
CS-Annotate: A Tool for Using NMR Chemical Shifts to Annotate RNA Structure. 1545-1549 - Norberto Sánchez-Cruz
, José L. Medina-Franco
:
Epigenetic Target Profiler: A Web Server to Predict Epigenetic Targets of Small Molecules. 1550-1554 - Markus Hollander
, David J. N. P. Rasp
, Moomal Aziz, Volkhard Helms
:
ProPores2: Web Service and Stand-Alone Tool for Identifying, Manipulating, and Visualizing Pores in Protein Structures. 1555-1559 - Xinhao Li
, Denis Fourches
:
SMILES Pair Encoding: A Data-Driven Substructure Tokenization Algorithm for Deep Learning. 1560-1569 - Tian Cai, Hansaim Lim, Kyra Alyssa Abbu
, Yue Qiu, Ruth Nussinov
, Lei Xie:
MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization. 1570-1582 - Derek Jones
, Hyojin Kim
, Xiaohua Zhang
, Adam T. Zemla, Garrett Stevenson
, W. F. Drew Bennett
, Daniel A. Kirshner
, Sergio Ernesto Wong, Felice C. Lightstone, Jonathan E. Allen
:
Improved Protein-Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference. 1583-1592 - Yuanqing Tang, Zhi Li, Mansoor Ani Najeeb Nellikkal
, Hamed Eramian, Emory M. Chan
, Alexander J. Norquist, D. Frank Hsu, Joshua Schrier
:
Improving Data and Prediction Quality of High-Throughput Perovskite Synthesis with Model Fusion. 1593-1602 - Eric J. Martin
, Xiang-Wei Zhu
:
Collaborative Profile-QSAR: A Natural Platform for Building Collaborative Models among Competing Companies. 1603-1616 - Junjie Wee
, Kelin Xia
:
Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein-Ligand Binding Affinity Prediction. 1617-1626 - Jiahao Wang
, Shuangjia Zheng
, Jianwen Chen
, Yuedong Yang
:
Meta Learning for Low-Resource Molecular Optimization. 1627-1636 - Pingshi Yu, Alistair J. Sterling
, Jotun Hein:
A Novel Automated Screening Method for Combinatorially Generated Small Molecules. 1637-1646 - Kiyoto Aramis Tanemura
, Susanta Das
, Kenneth M. Merz Jr.
:
AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations. 1647-1656 - Angela Lopez-del Rio
, Sergio Picart-Armada
, Alexandre Perera-Lluna:
Balancing Data on Deep Learning-Based Proteochemometric Activity Classification. 1657-1669 - Fen Pei
, Qingya Shi
, Haotian Zhang
, Ivet Bahar
:
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. 1670-1682 - Olga A. Tarasova
, Nadezhda Yu. Biziukova
, Anastassia V. Rudik
, Alexander V. Dmitriev, Dmitry Filimonov
, Vladimir Poroikov
:
Extraction of Data on Parent Compounds and Their Metabolites from Texts of Scientific Abstracts. 1683-1690 - Jian Jiang, Rui Wang
, Guo-Wei Wei
:
GGL-Tox: Geometric Graph Learning for Toxicity Prediction. 1691-1700 - Jiaru Bai
, Rory Geeson
, Feroz Farazi
, Sebastian Mosbach
, Jethro Akroyd
, Eric J. Bringley
, Markus Kraft
:
Automated Calibration of a Poly(oxymethylene) Dimethyl Ether Oxidation Mechanism Using the Knowledge Graph Technology. 1701-1717 - Peng Zhou
, Qian Liu, Ting Wu, Qingqing Miao, Shuyong Shang, Heyi Wang, Zheng Chen, Shaozhou Wang, Heyan Wang:
Systematic Comparison and Comprehensive Evaluation of 80 Amino Acid Descriptors in Peptide QSAR Modeling. 1718-1731 - Geoffrey R. Weal
, Samantha M. McIntyre
, Anna L. Garden
:
Development of a Structural Comparison Method to Promote Exploration of the Potential Energy Surface in the Global Optimization of Nanoclusters. 1732-1744 - James S. Peerless, Albert L. Kwansa, Branden S. Hawkins, Ralph C. Smith
, Yaroslava G. Yingling
:
Uncertainty Quantification and Sensitivity Analysis of Partial Charges on Macroscopic Solvent Properties in Molecular Dynamics Simulations with a Machine Learning Model. 1745-1761 - Malkeet Singh Bahia, Netaly Khazanov, Qingxian Zhou, Zhengrong Yang
, Chi Wang, Jeong S. Hong, Andras Rab, Eric Sorscher, Christel Brouillette, John F. Hunt, Hanoch Senderowitz
:
Stability Prediction for Mutations in the Cytosolic Domains of Cystic Fibrosis Transmembrane Conductance Regulator. 1762-1777 - Jonathan R. Heal
, Joseph M. Sheridan
, Manisha Kulkarni, Neill Liptrott
, Deirdre Egan, Saye Khoo, Ian Matthews, William D. O. Hamilton:
AUTOSTERE: Systematic Search for Scaffold Replacement Opportunities within Structural Databases. 1778-1788 - Francisco Adasme-Carreño
, Julio Caballero
, Joel Ireta
:
PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations. 1789-1800 - Hrvoje Rimac
, Maria A. Grishina, Vladimir Potemkin:
Use of the Complementarity Principle in Docking Procedures: A New Approach for Evaluating the Correctness of Binding Poses. 1801-1813 - Xavier Rozanska, Erich Wimmer, Frédérick de Meyer
:
Quantitative Kinetic Model of CO2 Absorption in Aqueous Tertiary Amine Solvents. 1814-1824 - Neethinathan Johnee Britto, Murugesan Panneerselvam, Madhu Deepan Kumar, Arunkumar Kathiravan
, Madhavan Jaccob
:
Substituent Effect on the Photophysics and ESIPT Mechanism of N, N′-Bis(salicylidene)-p-phenylenediamine: A DFT/TD-DFT Analysis. 1825-1839 - Sofia R. G. Camilo, Felipe Curtolo
, Vanesa V. Galassi
, Guilherme Menegon Arantes
:
Tunneling and Nonadiabatic Effects on a Proton-Coupled Electron Transfer Model for the Qo Site in Cytochrome bc1. 1840-1849 - Leena Aggarwal, Parbati Biswas
:
Hydration Thermodynamics of Familial Parkinson's Disease-Linked Mutants of α-Synuclein. 1850-1858 - Joanna M. Zarnecka
, Iva Lukac, Stephen J. Messham, Alhusein Hussin, Francesco Coppola
, Steven J. Enoch
, Alexander G. Dossetter
, Edward J. Griffen
, Andrew G. Leach
:
Mapping Ligand-Shape Space for Protein-Ligand Systems: Distinguishing Key-in-Lock and Hand-in-Glove Proteins. 1859-1874 - Antonella Paladino
, Fulvio D'Angelo
, Teresa Maria Rosaria Noviello
, Antonio Iavarone, Michele Ceccarelli
:
Structural Model for Recruitment of RIT1 to the LZTR1 E3 Ligase: Evidences from an Integrated Computational Approach. 1875-1888 - Xinghang Yuan
, Di Zhang, Shengjun Mao, Qiantao Wang
:
Filling the Gap in Understanding the Mechanism of GABAAR and Propofol Using Computational Approaches. 1889-1901 - Caroline S. Pereira
, Rodrigo L. Silveira
, Munir S. Skaf
:
QM/MM Simulations of Enzymatic Hydrolysis of Cellulose: Probing the Viability of an Endocyclic Mechanism for an Inverting Cellulase. 1902-1912 - Luis F. Ponce
, Galia Montalvo, Kalet Leon
, Pedro A. Valiente
:
Differential Effects of IL2Rα and IL15Rα over the Stability of the Common Beta-Gamma Signaling Subunits of the IL2 and IL15 Receptors. 1913-1920 - Kei Moritsugu
, Koh Takeuchi
, Narutoshi Kamiya
, Junichi Higo
, Isao Yasumatsu
, Yoshifumi Fukunishi, Ikuo Fukuda:
Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation. 1921-1930 - Anderson A. Gomes
, Gustavo F. da Silva
, Sirish Kaushik Lakkaraju
, Beatriz Gomes Guimarães
, Alexander D. MacKerell Jr.
, Maria de Lourdes B. Magalhães
:
Insights into Glucose-6-phosphate Allosteric Activation of β-Glucosidase A. 1931-1941 - Jon Uranga
, Lukas Hasecke
, Jonny Proppe
, Jan Fingerhut
, Ricardo A. Mata
:
Theoretical Studies of the Acid-Base Equilibria in a Model Active Site of the Human 20S Proteasome. 1942-1953 - Jianzhong Chen
, Shaolong Zhang, Wei Wang, Laixue Pang, Qinggang Zhang, Xinguo Liu:
Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis. 1954-1969 - David Shorthouse
, Michael W. J. Hall
, Benjamin A. Hall
:
Computational Saturation Screen Reveals the Landscape of Mutations in Human Fumarate Hydratase. 1970-1980 - Octav Caldararu, Tom L. Blundell, Kasper P. Kepp
:
Three Simple Properties Explain Protein Stability Change upon Mutation. 1981-1988 - Atanu Maity, Asha Rani Choudhury
, Rajarshi Chakrabarti
:
Effect of Stapling on the Thermodynamics of mdm2-p53 Binding. 1989-2000 - Giuseppe Deganutti
, Kerry Barkan, Graham Ladds
, Christopher A. Reynolds
:
Multisite Model of Allosterism for the Adenosine A1 Receptor. 2001-2015 - Jorge Gálvez
, Riccardo Zanni
, María Gálvez-Llompart
, José María Benlloch:
Macrolides May Prevent Severe Acute Respiratory Syndrome Coronavirus 2 Entry into Cells: A Quantitative Structure Activity Relationship Study and Experimental Validation. 2016-2025 - João Morado
, Paul N. Mortenson
, Marcel L. Verdonk
, Richard A. Ward
, Jonathan W. Essex
, Chris-Kriton Skylaris
:
ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields. 2026-2047 - Yadiris García, Brandon A. Úsuga, Cristian H. Campos
, Joel B. Alderete, Verónica A. Jiménez
:
NanoMIPs Design for Fucose and Mannose Recognition: A Molecular Dynamics Approach. 2048-2061 - Giorgio Amendola
, Roberta Ettari
, Santo Previti
, Carla Di Chio, Anna Messere, Salvatore Di Maro
, Stefan J. Hammerschmidt
, Collin Zimmer
, Robert A. Zimmermann
, Tanja Schirmeister, Maria Zappalà
, Sandro Cosconati
:
Lead Discovery of SARS-CoV-2 Main Protease Inhibitors through Covalent Docking-Based Virtual Screening. 2062-2073 - Hongyi Zhou, Hongnan Cao, Jeffrey Skolnick
:
FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening. 2074-2089 - C. K. Sruthi
, Meher K. Prakash
:
Disentangling the Contribution of Each Descriptive Characteristic of Every Single Mutation to Its Functional Effects. 2090-2098 - Dong-Gun Kim
, Yoonjoo Choi
, Hak-Sung Kim
:
Epitopes of Protein Binders Are Related to the Structural Flexibility of a Target Protein Surface. 2099-2107
Volume 61, Number 5, May 2021
- Issue Publication Information.
- Issue Editorial Masthead.
- Vinícius Wilian D. Cruzeiro
, Madushanka Manathunga
, Kenneth M. Merz Jr.
, Andreas W. Götz
:
Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK. 2109-2115 - Haohao Fu
, Haochuan Chen
, Wensheng Cai
, Xueguang Shao
, Christophe Chipot
:
BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations. 2116-2123 - Lauren Nelson, Sofia Bariami, Chris Ringrose, Joshua T. Horton
, Vadiraj Kurdekar, Antonia S. J. S. Mey
, Julien Michel, Daniel J. Cole
:
Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations. 2124-2130 - Cigdem Altintas, Omer Faruk Altundal
, Seda Keskin
, Ramazan Yildirim:
Machine Learning Meets with Metal Organic Frameworks for Gas Storage and Separation. 2131-2146 - Phan Nguyen
, Donald Loveland, Joanne Taery Kim, Piyush Karande
, Anna M. Hiszpanski
, Thomas Yong-Jin Han
:
Predicting Energetics Materials' Crystalline Density from Chemical Structure by Machine Learning. 2147-2158 - Raghuram Srinivas
, Niraj Verma, Elfi Kraka, Eric C. Larson:
Deep Learning-Based Ligand Design Using Shared Latent Implicit Fingerprints from Collaborative Filtering. 2159-2174 - Antonina L. Nazarova
, Liqiu Yang, Kuang Liu, Ankit Mishra, Rajiv K. Kalia, Ken-ichi Nomura, Aiichiro Nakano
, Priya Vashishta
, Pankaj Rajak:
Dielectric Polymer Property Prediction Using Recurrent Neural Networks with Optimizations. 2175-2186 - Arpan Mukherjee
, An Su
, Krishna Rajan
:
Deep Learning Model for Identifying Critical Structural Motifs in Potential Endocrine Disruptors. 2187-2197 - Colin Michael Van Oort, Jonathon B. Ferrell, Jacob M. Remington, Safwan Wshah, Jianing Li
:
AMPGAN v2: Machine Learning-Guided Design of Antimicrobial Peptides. 2198-2207 - Jinlong Li, Dongdong Peng, Yun Xie, Zong Dai
, Xiaoyong Zou
, Zhanchao Li
:
Novel Potential Small Molecule-MiRNA-Cancer Associations Prediction Model Based on Fingerprint, Sequence, and Clinical Symptoms. 2208-2219 - Robert C. Spiers
, John H. Kalivas
:
Reliable Model Selection without Reference Values by Utilizing Model Diversity with Prediction Similarity. 2220-2230 - Jingxiao Bao, Xiao He
, John Z. H. Zhang
:
DeepBSP - a Machine Learning Method for Accurate Prediction of Protein-Ligand Docking Structures. 2231-2240 - Maria J. Falaguera
, Jordi Mestres
:
Identification of the Core Chemical Structure in SureChEMBL Patents. 2241-2247 - Sarah Naomi Bolz
, Melissa F. Adasme
, Michael Schroeder:
Toward an Understanding of Pan-Assay Interference Compounds and Promiscuity: A Structural Perspective on Binding Modes. 2248-2262 - Veselina Marinova, Laurence Dodd, Song-Jun Lee, Geoffrey P. F. Wood
, Ivan Marziano, Matteo Salvalaglio
:
Identifying Conformational Isomers of Organic Molecules in Solution via Unsupervised Clustering. 2263-2273 - Anatoliy Kuznetsov, Nikolaos V. Sahinidis
:
ExtractionScore: A Quantitative Framework for Evaluating Synthetic Routes on Predicted Liquid-Liquid Extraction Performance. 2274-2282 - Lim Heo, Sangwoo Park, Chaok Seok
:
GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential. 2283-2293 - Krys E. A. Batista
, Marinalva D. Soares, Marcos G. Quiles
, Maurício J. Piotrowski
, Juarez L. F. Da Silva
:
Energy Decomposition to Access the Stability Changes Induced by CO Adsorption on Transition-Metal 13-Atom Clusters. 2294-2301 - Son Tung Ngo
, Nguyen Minh Tam
, Minh Quan Pham
, Trung Hai Nguyen
:
Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro. 2302-2312 - Ryan W. Kung
, Trinity K. Deak
, Cassidy A. Griffith-Salik
, Nathania A. Takyi
, Stacey D. Wetmore
:
Impact of DNA Adduct Size, Number, and Relative Position on the Toxicity of Aromatic Amines: A Molecular Dynamics Case Study of ANdG- and APdG-Containing DNA Duplexes. 2313-2327 - Juan M. Hernández-Meza
, Sergio Mares Sámano, Ramón Garduño-Juárez
:
Insights into the Molecular Inhibition of the Oncogenic Channel KV10.1 by Globular Toxins. 2328-2340 - Francois Berenger
, Ashutosh Kumar
, Kam Y. J. Zhang
, Yoshihiro Yamanishi:
Lean-Docking: Exploiting Ligands' Predicted Docking Scores to Accelerate Molecular Docking. 2341-2352 - Yunhui Ge
, Si Zhang
, Mate Erdelyi
, Vincent A. Voelz
:
Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2. 2353-2367 - Brahm J. Yachnin
, Vikram Khipple Mulligan
, Sagar D. Khare
, Chris Bailey-Kellogg
:
MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform. 2368-2382 - Christina Nutschel, Cristina Coscolín, Benoit David
, Daniel Mulnaes, Manuel Ferrer
, Karl-Erich Jaeger, Holger Gohlke
:
Promiscuous Esterases Counterintuitively Are Less Flexible than Specific Ones. 2383-2395 - Liang Qu, Xinyue Qiao, Fei Qi, Noritaka Nishida, Tyuji Hoshino
:
Analysis of Binding Modes of Antigen-Antibody Complexes by Molecular Mechanics Calculation. 2396-2406 - Mariia Nemchinova, Josef Melcr
, Tsjerk A. Wassenaar, Siewert J. Marrink
, Albert Guskov
:
Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations. 2407-2417 - Junhao Li, Yue Chen, Yun Tang
, Weihua Li, Yaoquan Tu
:
Homotropic Cooperativity of Midazolam Metabolism by Cytochrome P450 3A4: Insight from Computational Studies. 2418-2426 - Ai Shinobu, Chigusa Kobayashi
, Yasuhiro Matsunaga
, Yuji Sugita
:
Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins. 2427-2443 - Elif Naz Bingöl
, Onur Serçinoglu
, Pemra Ozbek
:
Unraveling the Allosteric Communication Mechanisms in T-Cell Receptor-Peptide-Loaded Major Histocompatibility Complex Dynamics Using Molecular Dynamics Simulations: An Approach Based on Dynamic Cross Correlation Maps and Residue Interaction Energy Calculations. 2444-2453 - Yan-jing Sheng, Yue-wen Yin
, Yu-Qing Ma
, Hong-ming Ding
:
Improving the Performance of MM/PBSA in Protein-Protein Interactions via the Screening Electrostatic Energy. 2454-2462 - Verónica A. Jiménez
, Karen R. Navarrete, Mario Duque-Noreña, Kelly P. Marrugo
, María A. Contreras, Cristian H. Campos
, Joel B. Alderete:
Rational Design of Novel Glycomimetic Peptides for E-Selectin Targeting. 2463-2474 - Jiye Wang
, Zengrui Wu
, Yayuan Peng
, Weihua Li
, Guixia Liu
, Yun Tang
:
Pathway-Based Drug Repurposing with DPNetinfer: A Method to Predict Drug-Pathway Associations via Network-Based Approaches. 2475-2485 - Zengrui Wu
, Qiaohui Wang, Hongbin Yang, Jiye Wang
, Weihua Li
, Guixia Liu
, Yi Yang
, Yuzheng Zhao
, Yun Tang
:
Discovery of Natural Products Targeting NQO1 via an Approach Combining Network-Based Inference and Identification of Privileged Substructures. 2486-2498 - Xiaoyu Wang, Xinben Zhang, Cheng Peng, Yulong Shi, Huiyu Li
, Zhijian Xu
, Weiliang Zhu
:
D3DistalMutation: a Database to Explore the Effect of Distal Mutations on Enzyme Activity. 2499-2508 - Jamie R. Nuñez, Monee Y. McGrady, Yasemin Yesiltepe, Ryan S. Renslow
, Thomas O. Metz
:
Correction to "Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets". 2509-2510
Volume 61, Number 6, June 2021
- Issue Editorial Masthead.
- Issue Publication Information.
- Marco Marcia
, Jacopo Manigrasso
, Marco de Vivo
:
Finding the Ion in the RNA-Stack: Can Computational Models Accurately Predict Key Functional Elements in Large Macromolecular Complexes? 2511-2515 - Renan P. O. Costa, Lucas Fernandes Lucena
, Lorena Mara A. Silva
, Guilherme Julião Zocolo
, Chonny Herrera-Acevedo, Luciana Scotti
, Fernando Batista Da-Costa
, Nikita Ionov
, Vladimir Poroikov
, Eugene N. Muratov
, Marcus Tulius Scotti
:
The SistematX Web Portal of Natural Products: An Update. 2516-2522 - Harrison Green, Jacob D. Durrant
:
DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization. 2523-2529 - Paul G. Francoeur
, David Ryan Koes
:
SolTranNet-A Machine Learning Tool for Fast Aqueous Solubility Prediction. 2530-2536 - Florian Leidner, Nese Kurt Yilmaz
, Celia A. Schiffer
:
Deciphering Antifungal Drug Resistance in Pneumocystis jirovecii DHFR with Molecular Dynamics and Machine Learning. 2537-2541 - Masakazu Matsumoto
, Takuma Yagasaki
, Hideki Tanaka
:
Novel Algorithm to Generate Hydrogen-Disordered Ice Structures. 2542-2546 - Alan E. Bilsland
, Kirsten McAulay
, Ryan West, Angelo Pugliese, Justin Bower:
Automated Generation of Novel Fragments Using Screening Data, a Dual SMILES Autoencoder, Transfer Learning and Syntax Correction. 2547-2559 - Allison S. Walker
, Jon Clardy
:
A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters. 2560-2571 - Jie Zhang
, Rocío Mercado, Ola Engkvist
, Hongming Chen:
Comparative Study of Deep Generative Models on Chemical Space Coverage. 2572-2581 - Chunming Yang
, Jie Chen, Runwen Wang, Miao Zhang, Chaoyang Zhang, Jian Liu
:
Density Prediction Models for Energetic Compounds Merely Using Molecular Topology. 2582-2593 - Charles McGill
, Michael Forsuelo, Yanfei Guan, William H. Green Jr.
:
Predicting Infrared Spectra with Message Passing Neural Networks. 2594-2609 - Jaswinder Singh
, Kuldip K. Paliwal
, Jaspreet Singh, Yaoqi Zhou
:
RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks. 2610-2622 - Carmen Esposito
, Gregory A. Landrum
, Nadine Schneider
, Nikolaus Stiefl
, Sereina Riniker
:
GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning. 2623-2640 - Kushal Batra, Kimberley M. Zorn, Daniel H. Foil
, Eni Minerali, Victor O. Gawriljuk, Thomas R. Lane, Sean Ekins
:
Quantum Machine Learning Algorithms for Drug Discovery Applications. 2641-2647 - Jin Zhang, Ulf Norinder
, Fredrik Svensson
:
Deep Learning-Based Conformal Prediction of Toxicity. 2648-2657 - Bruno Cuevas-Zuviría, Luis Fernández Pacios
:
Machine Learning of Analytical Electron Density in Large Molecules Through Message-Passing. 2658-2666 - Shree Hari Sureshbabu
, Manas Sajjan, Sangchul Oh
, Sabre Kais
:
Implementation of Quantum Machine Learning for Electronic Structure Calculations of Periodic Systems on Quantum Computing Devices. 2667-2674 - Srilatha Sakamuru
, Jinghua Zhao, Menghang Xia
, Huixiao Hong
, Anton Simeonov, Iosif I. Vaisman
, Ruili Huang
:
Predictive Models to Identify Small Molecule Activators and Inhibitors of Opioid Receptors. 2675-2685 - Mengjie Liu
, Alon Grinberg Dana
, Matthew S. Johnson, Mark J. Goldman
, Agnes Jocher
, A. Mark Payne, Colin A. Grambow
, Kehang Han
, Nathan W. Yee, Emily J. Mazeau
, Katrin Blondal
, Richard H. West
, C. Franklin Goldsmith
, William H. Green Jr.
:
Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation. 2686-2696 - Daiguo Deng, Xiaowei Chen, Ruochi Zhang, Zengrong Lei, Xiaojian Wang
, Fengfeng Zhou
:
XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties. 2697-2705 - Stefano Bonciarelli
, Jenny Desantis
, Laura Goracci
, Lydia Siragusa, Ismael Zamora
, Elisabeth Ortega-Carrasco
:
Automatic Identification of Lansoprazole Degradants under Stress Conditions by LC-HRMS with MassChemSite and WebChembase. 2706-2719 - Zhixiong Lin, Junjie Zou, Shuai Liu, Chunwang Peng, Zhipeng Li, Xiao Wan, Dong Fang, Jian Yin, Gianpaolo Gobbo
, Yongpan Chen, Jian Ma, Shuhao Wen, Peiyu Zhang, Mingjun Yang
:
A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Predictions: New Opportunities and Challenges for Drug Discovery. 2720-2732 - Zeynep Pinar Haslak
, Sabrina Zareb, Ilknur Dogan, Viktorya Aviyente
, Gerald Monard
:
Using Atomic Charges to Describe the pKa of Carboxylic Acids. 2733-2743 - Keisuke Yanagisawa
, Yoshitaka Moriwaki
, Tohru Terada
, Kentaro Shimizu:
EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation. 2744-2753 - Ting Gong, Jianfen Fan
:
Study on the Assembly Mechanisms and Transport Properties of Transmembrane End-Charged Cyclic Peptide Nanotubes. 2754-2765 - Dimitra-Danai Varsou
, Nikoletta-Maria Koutroumpa
, Haralambos Sarimveis
:
Automated Grouping of Nanomaterials and Read-Across Prediction of Their Adverse Effects Based on Mathematical Optimization. 2766-2779 - Alberto Ongaro
, Erika Oselladore
, Maurizio Memo
, Giovanni Ribaudo
, Alessandra Gianoncelli
:
Insight into the LFA-1/SARS-CoV-2 Orf7a Complex by Protein-Protein Docking, Molecular Dynamics, and MM-GBSA Calculations. 2780-2787 - Viet-Khoa Tran-Nguyen
, Guillaume Bret, Didier Rognan
:
True Accuracy of Fast Scoring Functions to Predict High-Throughput Screening Data from Docking Poses: The Simpler the Better. 2788-2797 - Qiyuan Zhao
, Nicolae C. Iovanac, Brett M. Savoie
:
Transferable Ring Corrections for Predicting Enthalpy of Formation of Cyclic Compounds. 2798-2805 - Zhifeng Jing
, Chengwen Liu
, Pengyu Y. Ren
:
Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition. 2806-2817 - Matthew F. D. Hurley, Justin D. Northrup, Yunhui Ge
, Christian E. Schafmeister
, Vincent A. Voelz
:
Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution. 2818-2828 - Hamed S. Hayatshahi
, Robert R. Luedtke, Michelle Taylor, Peng-Jen Chen, Benjamin E. Blass
, Jin Liu
:
Factors Governing Selectivity of Dopamine Receptor Binding Compounds for D2R and D3R Subtypes. 2829-2843 - Ercheng Wang
, Weitao Fu
, Dejun Jiang
, Huiyong Sun
, Junmei Wang
, Xujun Zhang, Gaoqi Weng, Hui Liu
, Peng Tao, Tingjun Hou
:
VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations. 2844-2856 - Maria Cecilia Oliveira
, Maksudbek Yusupov
, Annemie Bogaerts
, Rodrigo M. Cordeiro
:
Lipid Oxidation: Role of Membrane Phase-Separated Domains. 2857-2868 - Lisbeth Ravnkilde Kjølbye
, Leonardo De Maria
, Tsjerk A. Wassenaar
, Haleh Abdizadeh, Siewert J. Marrink
, Jesper Ferkinghoff-Borg, Birgit Schiøtt
:
General Protocol for Constructing Molecular Models of Nanodiscs. 2869-2883 - Andrei L. Lomize
, Kevin Schnitzer, Spencer C. Todd, Irina D. Pogozheva
:
Thermodynamics-Based Molecular Modeling of α-Helices in Membranes and Micelles. 2884-2896 - Daniel J. Evans
, Remy A. Yovanno
, Sanim Rahman
, David W. Cao
, Morgan Q. Beckett, Milan H. Patel, Afif F. Bandak, Albert Y. Lau
:
Finding Druggable Sites in Proteins Using TACTICS. 2897-2910 - Steven R. Shave
, Yan-Kai Chen
, Nhan T. Pham
, Manfred Auer
:
PyBindingCurve, Simulation, and Curve Fitting to Complex Binding Systems at Equilibrium. 2911-2915 - Huan He, Yuying Liu, Yunxiang Sun
, Feng Ding
:
Misfolding and Self-Assembly Dynamics of Microtubule-Binding Repeats of the Alzheimer-Related Protein Tau. 2916-2925 - Gábor Dániel Balogh, Tamás Gyöngyösi, István Timári
, Mihály Herczeg, Anikó Borbás, S. Kashif Sadiq, Krisztina Fehér
, Katalin E. Kövér
:
Conformational Analysis of Heparin-Analogue Pentasaccharides by Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulations. 2926-2936 - Mohammed H. Al Mughram, Claudio Catalano
, John P. Bowry, Martin K. Safo
, J. Neel Scarsdale, Glen E. Kellogg
:
3D Interaction Homology: Hydropathic Analyses of the "π-Cation" and "π-π" Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues. 2937-2956 - Shani Zev, Keren Raz, Renana Schwartz, Reem Tarabeh, Prashant Kumar Gupta
, Dan T. Major
:
Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro. 2957-2966 - Jing Xu, Federica Simonelli, Xiaoyun Li, Angelo Spinello
, Sara Laporte
, Vincent Torre, Alessandra Magistrato
:
Molecular Mechanisms of the Blockage of Glioblastoma Motility. 2967-2980 - Jiarong Peng
, Yongguang Zhang
, Yang Jiang
, Haiyang Zhang
:
Developing and Assessing Nonbonded Dummy Models of Magnesium Ion with Different Hydration Free Energy References. 2981-2997 - Malte Siemers, Ana-Nicoleta Bondar
:
Interactive Interface for Graph-Based Analyses of Dynamic H-Bond Networks: Application to Spike Protein S. 2998-3014 - Michel F. Sanner
, Khalid Zoghebi, Samara Hanna, Saghar Mozaffari, Simin Rahighi, Rakesh K. Tiwari
, Keykavous Parang
:
Cyclic Peptides as Protein Kinase Inhibitors: Structure-Activity Relationship and Molecular Modeling. 3015-3026 - Karina van den Broek, Matthias Epple
, Lisa Sophie Kersten, Hubert Kuhn, Achim Zielesny
:
Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation. 3027-3040 - Sergio Boneta
, Kemel Arafet, Vicent Moliner
:
QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate. 3041-3051 - Eric R. Hantz
, Steffen Lindert
:
Adaptative Steered Molecular Dynamics Study of Mutagenesis Effects on Calcium Affinity in the Regulatory Domain of Cardiac Troponin C. 3052-3057 - Eunice Cho, Margarida Rosa
, Ruhi Anjum, Saman Mehmood, Mariya Soban, Moniza Mujtaba, Khair Bux, Syed Tarique Moin
, Mohammad Tanweer, Sarath Dantu
, Alessandro Pandini
, Junqi Yin, Heng Ma, Arvind Ramanathan, Barira Islam
, Antonia S. J. S. Mey
, Debsindhu Bhowmik
, Shozeb M. Haider
:
Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites. 3058-3073 - Michel F. Sanner
, Leonard Dieguez, Stefano Forli
, Ewa Lis:
Improving Docking Power for Short Peptides Using Random Forest. 3074-3090 - María Gálvez-Llompart
, Riccardo Ocello, Laura Rullo, Serena Stamatakos
, Irene Alessandrini
, Riccardo Zanni
, Iñaki Tuñón
, Andrea Cavalli
, Sanzio Candeletti, Matteo Masetti
, Patrizia Romualdi
, Maurizio Recanatini
:
Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach. 3091-3108 - Alzbeta Türková
, Orsolya Ungvári, Réka Laczkó-Rigó, Erzsébet Mernyák, Gergely Szakács, Csilla Özvegy-Laczka, Barbara Zdrazil
:
Data-Driven Ensemble Docking to Map Molecular Interactions of Steroid Analogs with Hepatic Organic Anion Transporting Polypeptides. 3109-3127 - Siyang Tian
, Xuan Cao, Russell Greiner, Carin Li, Anchi Guo, David S. Wishart
:
CyProduct: A Software Tool for Accurately Predicting the Byproducts of Human Cytochrome P450 Metabolism. 3128-3140 - Sergio Alejandro Pinacho-Castellanos
, César R. García-Jacas
, Michael K. Gilson, Carlos A. Brizuela
:
Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. 3141-3157 - Atilio Reyes Romero, Angel Jonathan Ruiz-Moreno, Matthew R. Groves
, Marco Velasco-Velázquez
, Alexander S. Dömling
:
Correction to "Benchmark of Generic Shapes for Macrocycles". 3158
Volume 61, Number 7, July 2021
- Issue Publication Information.
- Issue Editorial Masthead.
- Xiaolin Pan
, Hao Wang, Cuiyu Li, John Z. H. Zhang
, Changge Ji
:
MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network. 3159-3165 - Martin Floor
, Kengjie Li, Miquel Estévez-Gay
, Luis Agulló
, Pau M. Muñoz-Torres
, Jenn K. Hwang, Sílvia Osuna
, Jordi Villà-Freixa
:
SBMOpenMM: A Builder of Structure-Based Models for OpenMM. 3166-3171 - Pietro G. A. Aronica
, Lauren M. Reid
, Nirali Desai, Jianguo Li
, Stephen J. Fox, Shilpa Yadahalli
, Jonathan W. Essex
, Chandra S. Verma
:
Computational Methods and Tools in Antimicrobial Peptide Research. 3172-3196 - Zachary J. Baum
, Xiang Yu, Philippe Y. Ayala, Yanan Zhao, Steven P. Watkins, Qiongqiong Zhou
:
Artificial Intelligence in Chemistry: Current Trends and Future Directions. 3197-3212 - Omar Casanova-Alvarez, Aliuska Morales Helguera, Miguel Ángel Cabrera-Pérez
, Reinaldo Molina Ruiz
, Christophe Molina
:
A Novel Automated Framework for QSAR Modeling of Highly Imbalanced Leishmania High-Throughput Screening Data. 3213-3231 - Nicole Beauregard, Maryam Pardakhti
, Ranjan Srivastava
:
In Silico Evolution of High-Performing Metal Organic Frameworks for Methane Adsorption. 3232-3239 - Mingyuan Xu
, Ting Ran
, Hongming Chen:
De Novo Molecule Design Through the Molecular Generative Model Conditioned by 3D Information of Protein Binding Sites. 3240-3254 - Marina Garcia de Lomana
, Andrea Morger
, Ulf Norinder
, Roland Buesen
, Robert Landsiedel
, Andrea Volkamer
, Johannes Kirchmair
, Miriam Mathea
:
ChemBioSim: Enhancing Conformal Prediction of In Vivo Toxicity by Use of Predicted Bioactivities. 3255-3272 - Mikolaj Sacha, Mikolaj Blaz, Piotr Byrski, Pawel Dabrowski-Tumanski
, Mikolaj Chrominski, Rafal Loska
, Pawel Wlodarczyk-Pruszynski, Stanislaw Jastrzebski
:
Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits. 3273-3284 - Shachar Fite, Omri Nitecki, Zeev Gross
:
Custom Tokenization Dictionary, CUSTODI: A General, Fast, and Reversible Data-Driven Representation and Regressor. 3285-3291 - Benjamin Bouvier
:
Protein-Protein Interface Topology as a Predictor of Secondary Structure and Molecular Function Using Convolutional Deep Learning. 3292-3303 - Biao Ma
, Kei Terayama
, Shigeyuki Matsumoto, Yuta Isaka, Yoko Sasakura, Hiroaki Iwata
, Mitsugu Araki
, Yasushi Okuno:
Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations. 3304-3313 - Raghad Al-Jarf, Alex G. C. de Sá, Douglas E. V. Pires
, David B. Ascher
:
pdCSM-cancer: Using Graph-Based Signatures to Identify Small Molecules with Anticancer Properties. 3314-3322 - Ningfeng Liu
, Junyong Lai
, Chuanyu Lyu
, Bo Qiang, Heyu Wang, Hongwei Jin, Liangren Zhang
, Zhenming Liu
:
Chemical Space, Scaffolds, and Halogenated Compounds of CMNPD: A Comprehensive Chemoinformatic Analysis. 3323-3336 - Marc J. Cawkwell
, Alexandra C. Burch
, Suyana R. Ferreira, Nicholas Lease
, Virginia W. Manner
:
Atom Equivalent Energies for the Rapid Estimation of the Heat of Formation of Explosive Molecules from Density Functional Tight Binding Theory. 3337-3347 - Hiroshi Nakano
, Tomoyuki Miyao
, Swarit Jasial
, Kimito Funatsu
:
Sparse Topological Pharmacophore Graphs for Interpretable Scaffold Hopping. 3348-3360 - Andreia Fortuna
, Paulo J. Costa
:
Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point Charges. 3361-3375 - Tianhao Yu, Emilia Olsson
, Guoping Lian, Lei Liu
, Feng Huo
, Xiangping Zhang
, Qiong Cai
:
Prediction of the Liquid-Liquid Extraction Properties of Imidazolium-Based Ionic Liquids for the Extraction of Aromatics from Aliphatics. 3376-3385 - Carles Martí
, Sarah Blanck
, Ruben Staub, Sophie Loehlé, Carine Michel
, Stephan N. Steinmann
:
DockOnSurf: A Python Code for the High-Throughput Screening of Flexible Molecules Adsorbed on Surfaces. 3386-3396 - Alessandra G. Ritacca
, Ida Ritacco, Eslam Dabbish
, Nino Russo
, Gloria Mazzone
, Emilia Sicilia
:
A Boron-Containing Compound Acting on Multiple Targets Against Alzheimer's Disease. Insights from Ab Initio and Molecular Dynamics Simulations. 3397-3410 - Felipe Orlando Morais
, Karla F. Andriani
, Juarez L. F. Da Silva
:
Investigation of the Stability Mechanisms of Eight-Atom Binary Metal Clusters Using DFT Calculations and k-means Clustering Algorithm. 3411-3420 - Daniel Cappel
, Jean-Christophe Mozziconacci, Tatjana Braun, Thomas Steinbrecher
:
Performance of Relative Binding Free Energy Calculations on an Automatically Generated Dataset of Halogen-Deshalogen Matched Molecular Pairs. 3421-3430 - Udit Gupta
, Dionisios G. Vlachos
:
Learning Chemistry of Complex Reaction Systems via a Python First-Principles Reaction Rule Stencil (pReSt) Generator. 3431-3441 - Shanthi Nagarajan
, Zu Yuan Qian, Parthiban Marimuthu
, Nabil J. Alkayed, Sanjiv Kaul, Anthony P. Barnes
:
Mapping the Molecular Architecture Required for Lipid-Binding Pockets Using a Subset of Established and Orphan G-Protein Coupled Receptors. 3442-3452 - Panagiotis C. Petris
, Paul Becherer, Johannes G. E. M. Fraaije:
Alkane/Water Partition Coefficient Calculation Based on the Modified AM1 Method and Internal Hydrogen Bonding Sampling Using COSMO-RS. 3453-3462 - Niklas E. Siedhoff
, Alexander-Maurice Illig
, Ulrich Schwaneberg
, Mehdi D. Davari
:
PyPEF - An Integrated Framework for Data-Driven Protein Engineering. 3463-3476 - Xiaotian Kong
, Enming Xing, Tony Zhuang, Pui-Kai Li
, Xiaolin Cheng
:
Mechanistic Insights into the Allosteric Inhibition of Androgen Receptors by Binding Function 3 Antagonists from an Integrated Molecular Modeling Study. 3477-3494 - Terra Sztain
, Rommie E. Amaro
, James Andrew McCammon
:
Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. 3495-3501 - Lionel Nauton
, Laurence Hecquet
, Vincent Théry
:
QM/MM Study of Human Transketolase: Thiamine Diphosphate Activation Mechanism and Complete Catalytic Cycle. 3502-3515 - Takaharu Mori
, Genki Terashi
, Daisuke Matsuoka, Daisuke Kihara
, Yuji Sugita
:
Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps. 3516-3528 - Yalong Cong
, Yinghui Feng, Hui Ni
, Fengdong Zhi, Yulu Miao, Bohuan Fang, Lujia Zhang
, John Z. H. Zhang
:
Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis. 3529-3542 - Sayyed Jalil Mahdizadeh
, Melissa Thomas
, Leif A. Eriksson
:
Reconstruction of the Fas-Based Death-Inducing Signaling Complex (DISC) Using a Protein-Protein Docking Meta-Approach. 3543-3558 - Saul Gonzalez-Resines, Peter J. Quinn, Richard J. Naftalin, Carmen Domene
:
Multiple Interactions of Glucose with the Extra-Membranous Loops of GLUT1 Aid Transport. 3559-3570 - Yejie Qiu
, Wenjie Shan, Haiyang Zhang
:
Force Field Benchmark of Amino Acids. 3. Hydration with Scaled Lennard-Jones Interactions. 3571-3582 - Kei Takedomi
, Masateru Ohta
, Toru Ekimoto, Mitsunori Ikeguchi
:
Effect of Water Molecules on the Activating S810L Mutation of the Mineralocorticoid Receptor. 3583-3592 - Eva Prasnikar
, Andrej Perdih
, Jure Borisek
:
All-Atom Simulations Reveal a Key Interaction Network in the HLA-E/NKG2A/CD94 Immune Complex Fine-Tuned by the Nonameric Peptide. 3593-3603 - Miquel A. Galmés, Katarzyna Swiderek
, Vicent Moliner
:
Computational Studies Suggest Promiscuous Candida antarctica Lipase B as an Environmentally Friendly Alternative for the Production of Epoxides. 3604-3614 - Izabela Ferreira, Sofie Slott, Kira Astakhova
, Gerald Weber
:
Complete Mesoscopic Parameterization of Single LNA Modifications in DNA Applied to Oncogene Probe Design. 3615-3624 - Toru Ekimoto, Takafumi Kudo, Tsutomu Yamane, Mitsunori Ikeguchi
:
Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations. 3625-3637 - Jingjing Wei, Yongjun Liu
:
Mechanistic Insights into the P450 TleB-Catalyzed Unusual Intramolecular C-N Bond Formation Involved in the Biosynthesis of Indolactam V. 3638-3648 - Pavel Janos
, Alessandra Magistrato
:
All-Atom Simulations Uncover the Molecular Terms of the NKCC1 Transport Mechanism. 3649-3658 - Aurélien F. A. Moumbock
, Jianyu Li
, Hoai T. T. Tran, Rahel Hinkelmann, Evelyn Lamy, Henning J. Jessen
, Stefan Günther
:
ePharmaLib: A Versatile Library of e-Pharmacophores to Address Small-Molecule (Poly-)Pharmacology. 3659-3666 - Giuseppina La Sala
, Anders Gunnarsson, Karl Edman, Christian Tyrchan
, Anders Hogner
, Andrey I. Frolov
:
Unraveling the Allosteric Cross-Talk between the Coactivator Peptide and the Ligand-Binding Site in the Glucocorticoid Receptor. 3667-3680 - Masatake Sugita
, Satoshi Sugiyama, Takuya Fujie
, Yasushi Yoshikawa, Keisuke Yanagisawa
, Masahito Ohue
, Yutaka Akiyama
:
Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations. 3681-3695 - Brendan Kelly, Scott A. Hollingsworth
, David C. Blakemore, Robert M. Owen
, R. Ian Storer, Nigel A. Swain
, Deniz Aydin
, Rubben Torella, Joseph S. Warmus, Ron O. Dror
:
Delineating the Ligand-Receptor Interactions That Lead to Biased Signaling at the μ-Opioid Receptor. 3696-3707 - Ariane Nunes-Alves
, Fabian Ormersbach, Rebecca C. Wade
:
Prediction of the Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis. 3708-3721 - Staffan Arvidsson McShane
, Ernst Ahlberg, Tobias Noeske
, Ola Spjuth
:
Machine Learning Strategies When Transitioning between Biological Assays. 3722-3733 - Arkajyoti Sengupta, Zhen Li
, Lin Frank Song
, Pengfei Li
, Kenneth M. Merz Jr.
:
Correction to "Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models". 3734-3735 - Sergio Alejandro Pinacho-Castellanos
, César R. García-Jacas
, Michael K. Gilson
, Carlos A. Brizuela
:
Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. 3736
Volume 61, Number 8, August 2021
- Issue Editorial Masthead.
- Issue Publication Information.
- Leonid Komissarov
, Robert Rüger
, Matti Hellström
, Toon Verstraelen
:
ParAMS: Parameter Optimization for Atomistic and Molecular Simulations. 3737-3743 - Hugo Guterres
, Sang-Jun Park
, Han Zhang
, Wonpil Im
:
CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement. 3744-3751 - H. Mert Polat
, Hirad S. Salehi
, Remco Hens, Dominika O. Wasik
, Ahmadreza Rahbari
, Frédérick de Meyer
, Céline Houriez, Christophe Coquelet
, Sofía Calero
, David Dubbeldam
, Othonas A. Moultos
, Thijs J. H. Vlugt
:
New Features of the Open Source Monte Carlo Software Brick-CFCMC: Thermodynamic Integration and Hybrid Trial Moves. 3752-3757 - Manuel A. Llanos
, Melisa E. Gantner
, Santiago Rodriguez
, Lucas N. Alberca, Carolina L. Bellera
, Alan Talevi
, Luciana Gavernet
:
Strengths and Weaknesses of Docking Simulations in the SARS-CoV-2 Era: the Main Protease (Mpro) Case Study. 3758-3770 - Hazem Mslati, Francesco Gentile
, Carl Perez, Artem Cherkasov
:
Comprehensive Consensus Analysis of SARS-CoV-2 Drug Repurposing Campaigns. 3771-3788 - Jiarui Chen, Hong-Hin Cheong, Shirley W. I. Siu
:
xDeep-AcPEP: Deep Learning Method for Anticancer Peptide Activity Prediction Based on Convolutional Neural Network and Multitask Learning. 3789-3803 - Victor O. Gawriljuk, Daniel H. Foil
, Ana C. Puhl
, Kimberley M. Zorn, Thomas R. Lane, Olga Riabova
, Vadim Makarov
, Andre S. Godoy
, Glaucius Oliva
, Sean Ekins
:
Development of Machine Learning Models and the Discovery of a New Antiviral Compound against Yellow Fever Virus. 3804-3813 - Igor Kozlovskii
, Petr Popov
:
Protein-Peptide Binding Site Detection Using 3D Convolutional Neural Networks. 3814-3823 - Zheng Tan
, Yan Li, Weimei Shi, Shiqing Yang:
A Multitask Approach to Learn Molecular Properties. 3824-3834 - Giorgio Amendola
, Sandro Cosconati
:
PyRMD: A New Fully Automated AI-Powered Ligand-Based Virtual Screening Tool. 3835-3845 - Michael Tynes
, Wenhao Gao
, Daniel J. Burrill, Enrique R. Batista
, Danny Perez
, Ping Yang
, Nicholas Lubbers:
Pairwise Difference Regression: A Machine Learning Meta-algorithm for Improved Prediction and Uncertainty Quantification in Chemical Search. 3846-3857 - Iljung Jin
, Hojung Nam
:
HiDRA: Hierarchical Network for Drug Response Prediction with Attention. 3858-3867 - Xiaochi Zhou, Daniel Nurkowski, Sebastian Mosbach
, Jethro Akroyd
, Markus Kraft
:
Question Answering System for Chemistry. 3868-3880 - Wagner E. Richter
, Leonardo J. Duarte
, Roy E. Bruns
:
Are "GAPT Charges" Really Just Charges? 3881-3890 - Jérôme Eberhardt, Diogo Santos-Martins
, Andreas F. Tillack
, Stefano Forli
:
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. 3891-3898 - Samuel Genheden
, Ola Engkvist
, Esben Jannik Bjerrum
:
Clustering of Synthetic Routes Using Tree Edit Distance. 3899-3907 - Oxana Andriuc
, Martin Siron
, Joseph H. Montoya
, Matthew K. Horton
, Kristin A. Persson
:
Automated Adsorption Workflow for Semiconductor Surfaces and the Application to Zinc Telluride. 3908-3916 - Jingyi Yang, Xiaoyuan Lin, Na Xing, Zhao Zhang, Haiwei Zhang, Haibo Wu
, Weiwei Xue
:
Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 Mpro. 3917-3926 - Smrithi Sundar, Avilasha A. Sandilya
, M. Hamsa Priya
:
Unraveling the Influence of Osmolytes on Water Hydrogen-Bond Network: From Local Structure to Graph Theory Analysis. 3927-3944 - Himansu S. Biswal
, Akshay Kumar Sahu, Antonio Frontera
, Antonio Bauzá
:
Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function. 3945-3954 - Osvaldo Yañez
, Rodrigo Báez-Grez
, Diego Inostroza
, Ricardo Pino-Rios
, Walter A. Rabanal-León
, Julia Contreras-Garcia, Carlos Cárdenas
, William Tiznado
:
Kick-Fukui: A Fukui Function-Guided Method for Molecular Structure Prediction. 3955-3963 - Thomas Giannos, Samo Lesnik, Urban Bren
, Milan Hodoscek
, Tatiana Domratcheva
, Ana-Nicoleta Bondar
:
CHARMM Force-Field Parameters for Morphine, Heroin, and Oliceridine, and Conformational Dynamics of Opioid Drugs. 3964-3977 - Zhiwei Yang
, Guoyin Li, Yizhen Zhao, Lei Zhang
, Xiaohui Yuan, Lingjie Meng
, Huadong Liu, Yong Han, Lintao Jia
, Shengli Zhang
:
Molecular Insights into the Recruiting Between UCP2 and DDX5/UBAP2L in the Metabolic Plasticity of Non-Small-Cell Lung Cancer. 3978-3987 - Nicole Balasco
, Josephine Alba
, Marco D'Abramo
, Luigi Vitagliano:
Quaternary Structure Transitions of Human Hemoglobin: An Atomic-Level View of the Functional Intermediate States. 3988-3999 - Yun Hao Feng
, Xiao Peng Zhang, Liu Fu Hu, Bo Zhi Chen
, Xin Dong Guo
:
Mesoscopic Simulation for the Effect of Cross-Linking Reactions on the Drug Diffusion Properties in Microneedles. 4000-4010 - Balázs Zoltán Zsidó
, Rita Börzsei, Viktor Szél, Csaba Hetényi
:
Determination of Ligand Binding Modes in Hydrated Viral Ion Channels to Foster Drug Design and Repositioning. 4011-4022 - Daniel Becker
, Prasad V. Bharatam, Holger Gohlke
:
F/G Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism. 4023-4030 - Yongguang Zhang
, Yang Jiang
, Jiarong Peng
, Haiyang Zhang
:
Rational Design of Nonbonded Point Charge Models for Divalent Metal Cations with Lennard-Jones 12-6 Potential. 4031-4044 - Hamid R. Kalhor
, Elham Taghikhani:
Probe into the Molecular Mechanism of Ibuprofen Interaction with Warfarin Bound to Human Serum Albumin in Comparison to Ascorbic and Salicylic Acids: Allosteric Inhibition of Anticoagulant Release. 4045-4057 - Jacob Al-Saleem
, Roger Granet, Srinivasan Ramakrishnan, Natalie A. Ciancetta, Catherine Saveson, Chris Gessner, Qiongqiong Zhou
:
Knowledge Graph-Based Approaches to Drug Repurposing for COVID-19. 4058-4067 - Illimar Hugo Rekand
, Ruth Brenk
:
DrugPred_RNA - A Tool for Structure-Based Druggability Predictions for RNA Binding Sites. 4068-4081 - Enrico Glaab
, Ganesh Babu Manoharan
, Daniel Abankwa
:
Pharmacophore Model for SARS-CoV-2 3CLpro Small-Molecule Inhibitors and in Vitro Experimental Validation of Computationally Screened Inhibitors. 4082-4096 - Janez Konc
, Samo Lesnik, Blaz Skrlj, Dusanka Janezic
:
ProBiS-Dock Database: A Web Server and Interactive Web Repository of Small Ligand-Protein Binding Sites for Drug Design. 4097-4107 - Sandhya P. Tiwari
, Florence Tama
, Osamu Miyashita:
Protocol for Retrieving Three-Dimensional Biological Shapes for a Few XFEL Single-Particle Diffraction Patterns. 4108-4119 - Paul G. Francoeur
, David Ryan Koes
:
Correction to "SolTranNet - A Machine Learning Tool for Fast Aqueous Solubility Prediction". 4120-4123 - Jiang Guo, A. Santiago Ibanez-Lopez, Hanyu Gao, Victor Quach, Connor W. Coley, Klavs F. Jensen
, Regina Barzilay:
Correction to Automated Chemical Reaction Extraction from Scientific Literature. 4124
Volume 61, Number 9, September 2021
- Issue Editorial Masthead.
- Issue Publication Information.
- Thomas R. Lane, Sean Ekins
:
Defending Antiviral Cationic Amphiphilic Drugs That May Cause Drug-Induced Phospholipidosis. 4125-4130 - Stamatia Zavitsanou
, Alexandros Tsengenes, Michail Papadourakis, Giorgio Amendola
, Alexios Chatzigoulas
, Dimitris Dellis, Sandro Cosconati
, Zoe Cournia
:
FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations. 4131-4138 - Michael Kilgour
, Tao Liu, Brandon D. Walker, Pengyu Y. Ren
, Lena Simine
:
E2EDNA: Simulation Protocol for DNA Aptamers with Ligands. 4139-4144 - Han Zhang
, Seonghoon Kim
, Timothy J. Giese
, Tai-Sung Lee
, Jumin Lee
, Darrin M. York
, Wonpil Im
:
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER. 4145-4151 - David Shorthouse
, Benjamin A. Hall
:
SARS-CoV-2 Variants Are Selecting for Spike Protein Mutations That Increase Protein Stability. 4152-4155 - Hamid Safizadeh
, Scott W. Simpkins, Justin Nelson, Sheena C. Li, Jeff S. Piotrowski, Mami Yoshimura, Yoko Yashiroda, Hiroyuki Hirano, Hiroyuki Osada
, Minoru Yoshida, Charles Boone, Chad L. Myers:
Improving Measures of Chemical Structural Similarity Using Machine Learning on Chemical-Genetic Interactions. 4156-4172 - Tahereh G. Avval, Behnam Moeini
, Victoria Carver, Neal Fairley, Emily F. Smith, Jonas Baltrusaitis
, Vincent Fernandez, Bonnie J. Tyler
, Neal Gallagher, Matthew R. Linford
:
The Often-Overlooked Power of Summary Statistics in Exploratory Data Analysis: Comparison of Pattern Recognition Entropy (PRE) to Other Summary Statistics and Introduction of Divided Spectrum-PRE (DS-PRE). 4173-4189 - Jason E. Sanchez, Govinda B. Kc, Julian Franco, William J. Allen, Jesus David Garcia, Suman Sirimulla
:
BiasNet: A Model to Predict Ligand Bias Toward GPCR Signaling. 4190-4199 - Liyuan Huang, Chen Ling
:
Leveraging Transfer Learning and Chemical Principles toward Interpretable Materials Properties. 4200-4209 - Luis Cesar de Azevedo
, Gabriel A. Pinheiro
, Marcos G. Quiles
, Juarez L. F. Da Silva
, Ronaldo C. Prati
:
Systematic Investigation of Error Distribution in Machine Learning Algorithms Applied to the Quantum-Chemistry QM9 Data Set Using the Bias and Variance Decomposition. 4210-4223 - Victor O. Gawriljuk, Phyo Phyo Kyaw Zin, Ana C. Puhl
, Kimberley M. Zorn, Daniel H. Foil
, Thomas R. Lane, Brett Hurst, Tatyana Almeida Tavella, Fabio Trindade Maranhão Costa, Premkumar Lakshmanane, Jean Bernatchez, Andre S. Godoy
, Glaucius Oliva
, Jair L. Siqueira-Neto, Peter B. Madrid, Sean Ekins
:
Machine Learning Models Identify Inhibitors of SARS-CoV-2. 4224-4235 - Aayush Gupta
, Huan-Xiang Zhou
:
Machine Learning-Enabled Pipeline for Large-Scale Virtual Drug Screening. 4236-4244 - Philippe Gantzer
, Benoît Creton
, Carlos Nieto-Draghi
:
Comparisons of Molecular Structure Generation Methods Based on Fragment Assemblies and Genetic Graphs. 4245-4258 - Junhui Lu, Huimin Zhang, Jinhui Yu, Dezun Shan, Ji Qi, Jiawen Chen, Hongwei Song
, Minghui Yang
:
Predicting Rate Constants of Hydroxyl Radical Reactions with Alkanes Using Machine Learning. 4259-4265 - Kuo-Hao Lee, Andrew D. Fant, Jiqing Guo, Andy Guan, Joslyn Jung, Mary Kudaibergenova, Williams E. Miranda, Therese Ku, Jianjing Cao, Soren Wacker
, Henry J. Duff, Amy Hauck Newman
, Sergei Yu Noskov
, Lei Shi
:
Toward Reducing hERG Affinities for DAT Inhibitors with a Combined Machine Learning and Molecular Modeling Approach. 4266-4279 - Juraj Mavracic
, Callum J. Court
, Taketomo Isazawa
, R. Stephen Elliott
, Jacqueline M. Cole
:
ChemDataExtractor 2.0: Autopopulated Ontologies for Materials Science. 4280-4289 - Lulu Zheng, Bin Zhu, Zengrui Wu
, Fang Liang, Minghuang Hong
, Guixia Liu
, Weihua Li
, Guobin Ren
, Yun Tang
:
SMINBR: An Integrated Network and Chemoinformatics Tool Specialized for Prediction of Two-Component Crystal Formation. 4290-4302 - Kazuma Kaitoh
, Yoshihiro Yamanishi:
TRIOMPHE: Transcriptome-Based Inference and Generation of Molecules with Desired Phenotypes by Machine Learning. 4303-4320 - Sarabjeet Kaur
, Payal Grover, Stacey D. Wetmore
, Purshotam Sharma
:
Role of Stacking Interactions in the Stability of Primitive Genetics: A Quantum Chemical View. 4321-4330 - Shuo Gu, Matthew S. Smith, Ying Yang, John J. Irwin, Brian K. Shoichet
:
Ligand Strain Energy in Large Library Docking. 4331-4341 - Steven Bennett, Filip T. Szczypinski
, Lukas Turcani, Michael E. Briggs
, Rebecca L. Greenaway
, Kim E. Jelfs
:
Materials Precursor Score: Modeling Chemists' Intuition for the Synthetic Accessibility of Porous Organic Cage Precursors. 4342-4356 - Xingyi Guan
, Itai Leven, Farnaz Heidar-Zadeh
, Teresa Head-Gordon
:
Protein C-GeM: A Coarse-Grained Electron Model for Fast and Accurate Protein Electrostatics Prediction. 4357-4369 - Gantulga Norjmaa
, Pietro Vidossich, Jean-Didier Maréchal
, Gregori Ujaque
:
Modeling Kinetics and Thermodynamics of Guest Encapsulation into the [M4L6]12- Supramolecular Organometallic Cage. 4370-4381 - Drazen Petrov
:
Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder. 4382-4390 - Daniele Veclani
, Marilena Tolazzi, José Pedro Cerón-Carrasco
, Andrea Melchior
:
Intercalation Ability of Novel Monofunctional Platinum Anticancer Drugs: A Key Step in Their Biological Action. 4391-4399 - Bridgette J. Befort
, Ryan S. DeFever
, Garrett M. Tow
, Alexander W. Dowling
, Edward J. Maginn
:
Machine Learning Directed Optimization of Classical Molecular Modeling Force Fields. 4400-4414 - José Manuel Vicent-Luna
, Sofia Apergi
, Shuxia Tao
:
Efficient Computation of Structural and Electronic Properties of Halide Perovskites Using Density Functional Tight Binding: GFN1-xTB Method. 4415-4424 - Bahaa Jawad
, Puja Adhikari, Rudolf Podgornik, Wai-Yim Ching
:
Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation. 4425-4441 - Debayan Dey, Suryanarayanarao Ramakumar, Graeme L. Conn
:
Targeted Redesign of Suramin Analogs for Novel Antimicrobial Lead Development. 4442-4454 - Marta Queizán, Marta Sánchez-Lozano, Marcos Mandado
, Jose Manuel Hermida-Ramón
:
A Highly Efficient Neutral Anion Receptor in Polar Environments by Synergy of Anion-π Interactions and Hydrogen Bonding. 4455-4461 - Duván González, Luis Macaya, Esteban Vöhringer-Martinez
:
Molecular Environment-Specific Atomic Charges Improve Binding Affinity Predictions of SAMPL5 Host-Guest Systems. 4462-4474 - Mateusz Marcisz, Martin Zacharias, Sergey A. Samsonov
:
Modeling Protein-Glycosaminoglycan Complexes: Does the Size Matter? 4475-4485 - Lucas S. R. Cavalcante
, Luke L. Daemen, Nir Goldman
, Adam J. Moulé
:
Davis Computational Spectroscopy Workflow - From Structure to Spectra. 4486-4496 - Javad Noroozi
, William R. Smith
:
Force-Field-Based Computational Study of the Thermodynamics of a Large Set of Aqueous Alkanolamine Solvents for Post-Combustion CO2 Capture. 4497-4513 - Dong Hyeon Mok
, Seoin Back
:
Atomic Structure-Free Representation of Active Motifs for Expedited Catalyst Discovery. 4514-4520 - Sachini P. Kadaoluwa Pathirannahalage, Nastaran Meftahi
, Aaron Elbourne
, Alessia C. G. Weiss
, Chris F. McConville
, Agilio Padua
, David A. Winkler
, Margarida Costa Gomes
, Tamar L. Greaves
, Tu C. Le
, Quinn A. Besford
, Andrew J. Christofferson
:
Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations. 4521-4536 - Juan M. Marmolejo-Tejada
, Jhonattan De La Roche-Yepes
, Carlos A. Pérez-López, Jaime Andres Perez-Taborda
, Alba Ávila
, Andrés Jaramillo-Botero
:
Understanding the Origin of Enhanced Piezoelectric Response in PVDF Matrices with Embedded ZnO Nanoparticles, from Polarizable Molecular Dynamics Simulations. 4537-4543 - Sergei F. Vyboishchikov
, Alexander A. Voityuk
:
Solvation Free Energies for Aqueous and Nonaqueous Solutions Computed Using PM7 Atomic Charges. 4544-4553 - Wayde Veldman
, Marcelo Vizona Liberato, Valquiria P. Souza, Vitor M. Almeida, Sandro R. Marana
, Özlem Tastan Bishop
, Igor Polikarpov
:
Differences in Gluco and Galacto Substrate-Binding Interactions in a Dual 6Pβ-Glucosidase/6Pβ-Galactosidase Glycoside Hydrolase 1 Enzyme from Bacillus licheniformis. 4554-4570 - Yan Guo, Noritaka Nishida, Tyuji Hoshino
:
Quantifying the Separation of Positive and Negative Areas in Electrostatic Potential for Predicting Feasibility of Ammonium Sulfate for Protein Crystallization. 4571-4581 - Santiago Movilla
, Sergio Martí
, Maite Roca
, Vicent Moliner
:
Unrevealing the Proteolytic Activity of RgpB Gingipain from Computational Simulations. 4582-4593 - Kaori Fukuzawa
, Koichiro Kato
, Chiduru Watanabe
, Yusuke Kawashima
, Yuma Handa
, Ami Yamamoto, Kazuki Watanabe
, Tatsuya Ohyama
, Kikuko Kamisaka
, Daisuke Takaya
, Teruki Honma
:
Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins. 4594-4612 - Yongguang Zhang
, Yang Jiang
, Yejie Qiu
, Haiyang Zhang
:
Rational Design of Nonbonded Point Charge Models for Highly Charged Metal Cations with Lennard-Jones 12-6 Potential. 4613-4629 - Chao Yang
, Yingkai Zhang
:
Lin_F9: A Linear Empirical Scoring Function for Protein-Ligand Docking. 4630-4644 - Aliasghar Sepehri, Binod Nepal, Themis Lazaridis
:
Distinct Modes of Action of IAPP Oligomers on Membranes. 4645-4655 - Brandon Havranek
, Kui K. Chan
, Austin Wu, Erik Procko, Shahidul M. Islam
:
Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity. 4656-4669 - Liqun Zhang
:
Interaction of Human β Defensin Type 3 (hBD-3) with Different PIP2-Containing Membranes, a Molecular Dynamics Simulation Study. 4670-4686 - Alice Triveri, Stefano A. Serapian
, Filippo Marchetti, Filippo Doria, Silvia Pavoni, Fabrizio Cinquini, Elisabetta Moroni, Andrea Rasola, Francesco Frigerio, Giorgio Colombo
:
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. 4687-4700 - Afrah Khairallah
, Caroline J. Ross, Özlem Tastan Bishop
:
GTP Cyclohydrolase I as a Potential Drug Target: New Insights into Its Allosteric Modulation via Normal Mode Analysis. 4701-4719 - Ying Yang, Lei Zhang, Jinying Tian, Fei Ye, Zhiyan Xiao
:
Integrated Approach to Identify Selective PTP1B Inhibitors Targeting the Allosteric Site. 4720-4732 - Vinícius Bonatto
, Anwar Shamim, Fernanda dos R. Rocho
, Andrei Leitão
, F. Javier Luque
, Jerônimo Lameira
, Carlos Alberto Montanari
:
Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations. 4733-4744 - Anjela Manandhar
, Vunnam Srinivasulu, Mohamad Hamad, Hamadeh Tarazi, Hany Omar
, Dennis J. Colussi, John Gordon, Wayne Childers, Michael L. Klein
, Taleb H. Al-Tel
, Magid Abou-Gharbia
, Khaled M. Elokely
:
Discovery of Novel Small-Molecule Inhibitors of SARS-CoV-2 Main Protease as Potential Leads for COVID-19 Treatment. 4745-4757 - Teresa Maria Creanza
, Pietro Delre
, Nicola Ancona
, Giovanni Lentini
, Michele Saviano
, Giuseppe Felice Mangiatordi
:
Structure-Based Prediction of hERG-Related Cardiotoxicity: A Benchmark Study. 4758-4770 - Yuyu Feng, Keqiong Zhang, Qilong Wu, Sheng-You Huang
:
NLDock: a Fast Nucleic Acid-Ligand Docking Algorithm for Modeling RNA/DNA-Ligand Complexes. 4771-4782 - Ivan A. Strelnikov
, Natalya A. Kovaleva, Elena A. Zubova
:
Variability of the DNA Backbone Geometry in DNA-Protein Complexes: Experimental Data Analysis. 4783-4794 - Yu-Xuan Chen
, Rui Xie, Yang Yang, Lin He, Dagan Feng, Hong-Bin Shen
:
Fast Cryo-EM Image Alignment Algorithm Using Power Spectrum Features. 4795-4806 - Panagiotis I. Koukos, Manon Réau, Alexandre M. J. J. Bonvin
:
Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. 4807-4818 - Zhixiong Lin, Junjie Zou, Shuai Liu, Chunwang Peng, Zhipeng Li, Xiao Wan, Dong Fang, Jian Yin, Gianpaolo Gobbo
, Yongpan Chen, Jian Ma, Shuhao Wen, Peiyu Zhang, Mingjun Yang
:
Correction to "A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Prediction: New Opportunities and Challenges for Drug Discovery". 4819 - Daiguo Deng, Xiaowei Chen, Ruochi Zhang, Zengrong Lei, Xiaojian Wang
, Fengfeng Zhou
:
Correction to "XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties". 4820-4822
Volume 61, Number 10, October 2021
- Issue Publication Information.
- Issue Editorial Masthead.
- Damjan Krstajic
:
Critical Assessment of Conformal Prediction Methods Applied in Binary Classification Settings. 4823-4826 - Jeffrey Skolnick
, Mu Gao, Hongyi Zhou, Suresh Singh:
AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function. 4827-4831 - Mustafa Tekpinar
, Bertrand Néron
, Marc Delarue:
Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus. 4832-4838 - Cristina González Fernández
, Arantza Basauri, Marcos Fallanza
, Eugenio Bringas
, Chris Oostenbrink
, Inmaculada Ortiz
:
Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review. 4839-4851 - Pablo R. Arantes
, Marcelo Depólo Polêto
, Conrado Pedebos
, Rodrigo Ligabue-Braun
:
Making it Rain: Cloud-Based Molecular Simulations for Everyone. 4852-4856 - David R. Bell
, Serena H. Chen
:
Toward Guided Mutagenesis: Gaussian Process Regression Predicts MHC Class II Antigen Mutant Binding. 4857-4867 - Fulvio Ciriaco
, Nicola Gambacorta, Domenico Alberga, Orazio Nicolotti
:
Quantitative Polypharmacology Profiling Based on a Multifingerprint Similarity Predictive Approach. 4868-4876 - Adam C. Mater
, Michelle L. Coote
:
Explainable Molecular Sets: Using Information Theory to Generate Meaningful Descriptions of Groups of Molecules. 4877-4889 - Samuel Boobier
, Yufeng Liu
, Krishna Sharma
, David R. J. Hose, A. John Blacker
, Nikil Kapur
, Bao N. Nguyen
:
Predicting Solvent-Dependent Nucleophilicity Parameter with a Causal Structure Property Relationship. 4890-4899 - Lizhao Hu, Yuyao Yang
, Shuangjia Zheng
, Jun Xu, Ting Ran
, Hongming Chen
:
Kinase Inhibitor Scaffold Hopping with Deep Learning Approaches. 4900-4912 - Dmitry V. Zankov
, Mariia Matveieva, Aleksandra V. Nikonenko, Ramil I. Nugmanov
, Igor I. Baskin
, Alexandre Varnek
, Pavel G. Polishchuk
, Timur I. Madzhidov
:
QSAR Modeling Based on Conformation Ensembles Using a Multi-Instance Learning Approach. 4913-4923 - Yueming Yin, Haifeng Hu
, Zhen Yang, Huajian Xu, Jiansheng Wu
:
RealVS: Toward Enhancing the Precision of Top Hits in Ligand-Based Virtual Screening of Drug Leads from Large Compound Databases. 4924-4939 - Andrei Y. Bochkov
, Philip V. Toukach
:
CSDB/SNFG Structure Editor: An Online Glycan Builder with 2D and 3D Structure Visualization. 4940-4948 - Esther Heid
, Samuel Goldman
, Karthik Sankaranarayanan
, Connor W. Coley
, Christoph Flamm
, William H. Green Jr.
:
EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. 4949-4961 - Damian M. Wilary, Jacqueline M. Cole
:
ReactionDataExtractor: A Tool for Automated Extraction of Information from Chemical Reaction Schemes. 4962-4974 - Mosavverul Hassan
, Evangelos A. Coutsias
:
Kinematic Reconstruction of Cyclic Peptides and Protein Backbones from Partial Data. 4975-5000 - Angelica Fierro
, Douglas J. Matthies
, Bruce K. Cassels
, Pablo Jaque
, Gerald Zapata-Torres
:
5-HT2 Receptor Subfamily and the Halogen Bond Promise. 5001-5012 - Bumjoon Seo
, Zih-Yu Lin
, Qiyuan Zhao
, Michael A. Webb
, Brett M. Savoie
:
Topology Automated Force-Field Interactions (TAFFI): A Framework for Developing Transferable Force Fields. 5013-5027 - Nezrina Mihovic
, Nevena Tomasevic
, Sanja Matic
, Marina M. Mitrovic, Danijela A. Kostic
, Manuela Sabatino, Lorenzo Antonini
, Rino Ragno
, Milan Mladenovic
:
Human Estrogen Receptor α Antagonists. Part 1: 3-D QSAR-Driven Rational Design of Innovative Coumarin-Related Antiestrogens as Breast Cancer Suppressants through Structure-Based and Ligand-Based Studies. 5028-5053 - Dawid Warszycki, Lukasz Struski, Marek Smieja, Rafal Kafel, Rafal Kurczab
:
Pharmacoprint: A Combination of a Pharmacophore Fingerprint and Artificial Intelligence as a Tool for Computer-Aided Drug Design. 5054-5065 - Jovan Damjanovic
, James M. Murphy, Yu-Shan Lin
:
CATBOSS: Cluster Analysis of Trajectories Based on Segment Splitting. 5066-5081 - Xue-Hui Guo, Li-Bo Yu, Xue-Li Hao, Tengfei He, Jing-Fu Guo, Xue Wei, Wei-Bo Cui, Li-Ying Yu, Zexing Qu
, Ai-Min Ren
:
Theoretical Study of a Two-Photon Fluorescent Probe Based on Nile Red Derivatives with Controllable Fluorescence Wavelength and Water Solubility. 5082-5097 - Eman Nabil
, Ahmed A. Hasanein, Rua B. Alnoman, Mohamed Zakaria
:
Optimizing the Cosensitization Effect of SQ02 Dye on BP-2 Dye-Sensitized Solar Cells: A Computational Quantum Chemical Study. 5098-5116 - Guillermo Goode-Romero, Laura Dominguez, Ana Martínez
:
Electron Donor-Acceptor Properties of Different Muscarinic Ligands: On the Road to Control Schizophrenia. 5117-5124 - Maria G. Khrenova, Fedor D. Mulashkin, Alexander V. Nemukhin
:
Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation. 5125-5132 - Shufeng Liu, Tien Huynh, Charles B. Stauft, Tony T. Wang, Binquan Luan
:
Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. 5133-5140 - Junxi Mu, Zhengsong Pan, Hai-Feng Chen
:
Balanced Solvent Model for Intrinsically Disordered and Ordered Proteins. 5141-5151 - Mert Golcuk, Aysima Hacisuleyman, Burak Erman
, Ahmet Yildiz, Mert Gur:
Binding Mechanism of Neutralizing Nanobodies Targeting SARS-CoV-2 Spike Glycoprotein. 5152-5160 - Gert-Jan Bekker
, Mitsugu Araki
, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
:
Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking. 5161-5171 - Gennady M. Verkhivker
, Steve Agajanian, Deniz Yasar Oztas, Grace Gupta:
Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and Signaling. 5172-5191 - Soohyung Park
, Yeol Kyo Choi
, Seonghoon Kim
, Jumin Lee
, Wonpil Im
:
CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids. 5192-5202 - Binbin Chen
, Zhengzhong Kang
, En Zheng, Yingchun Liu
, James W. Gauld
, Qi Wang
:
Hydrolysis Mechanism of the Linkers by Matrix Metalloproteinase-9 Using QM/MM Calculations. 5203-5211 - Xiaohui Wang
:
Conformational Fluctuations in GTP-Bound K-Ras: A Metadynamics Perspective with Harmonic Linear Discriminant Analysis. 5212-5222 - Bin Sun
, Xuan Fang
, Christopher N. Johnson
, Garrett Hauck
, Yongjun Kou, Jonathan P. Davis, Peter M. Kekenes-Huskey
:
Non-Canonical Interaction between Calmodulin and Calcineurin Contributes to the Differential Regulation of Plant-Derived Calmodulins on Calcineurin. 5223-5233 - Ernest Awoonor-Williams
, Christopher N. Rowley:
Modeling the Binding and Conformational Energetics of a Targeted Covalent Inhibitor to Bruton's Tyrosine Kinase. 5234-5242 - Indu Negi, Amanpreet Singh Mahmi, Preethi Seelam Prabhakar, Purshotam Sharma
:
Molecular Dynamics Simulations of the Aptamer Domain of Guanidinium Ion Binding Riboswitch ykkC-III: Structural Insights into the Discrimination of Cognate and Alternate Ligands. 5243-5255 - Roberto Fino
, Dominik Lenhart, Vishal C. Kalel
, Charlotte A. Softley
, Valeria Napolitano
, Ryan Byrne, Wolfgang Schliebs
, Maciej Dawidowski
, Ralf Erdmann, Michael Sattler
, Gisbert Schneider
, Oliver Plettenburg
, Grzegorz M. Popowicz
:
Computer-Aided Design and Synthesis of a New Class of PEX14 Inhibitors: Substituted 2, 3, 4, 5-Tetrahydrobenzo[F][1, 4]oxazepines as Potential New Trypanocidal Agents. 5256-5268 - Hengzhi Sun, Jinzheng Wang, Shengjie Liu, Xinyu Zhou, Liang Dai
, Caiping Chen, Qinglong Xu
, Xiaoan Wen
, Keguang Cheng
, Hongbin Sun
, Haoliang Yuan
:
Discovery of Novel Small Molecule Inhibitors Disrupting the PCSK9-LDLR Interaction. 5269-5279 - Maryam Rouhani
, Hamid Hadi-Alijanvand
:
Effect of Lithium Drug on Binding Affinities of Glycogen Synthase Kinase-3 β to Its Network Partners: A New Computational Approach. 5280-5292 - Kornel Ozvoldik
, Thomas Stockner
, Burkhard Rammner, Elmar Krieger
:
Assembly of Biomolecular Gigastructures and Visualization with the Vulkan Graphics API. 5293-5303
Volume 61, Number 11, November 2021
- Issue Editorial Masthead.
- Issue Publication Information.
- Zoe Cournia
, Thereza A. Soares
, Habibah A. Wahab
, Rommie E. Amaro
:
Advancing Women in Chemistry. 5305-5306 - Yun Lyna Luo
:
Mechanism-Based and Computational-Driven Covalent Drug Design. 5307-5311 - Yifan Wang
, Tai-Ying Chen, Dionisios G. Vlachos
:
NEXTorch: A Design and Bayesian Optimization Toolkit for Chemical Sciences and Engineering. 5312-5319 - Marina Macchiagodena
, Maurice Karrenbrock
, Marco Pagliai
, Piero Procacci
:
Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS. 5320-5326 - Jianyu Li
, Aurélien F. A. Moumbock
, Ammar Qaseem, Qianqing Xu
, Yue Feng, Dan Wang, Stefan Günther
:
AroCageDB: A Web-Based Resource for Aromatic Cage Binding Sites and Their Intrinsic Ligands. 5327-5330 - Mark D. Driver
, Mark J. Williamson, Nicola De Mitri
, Teodor Nikolov, Christopher A. Hunter:
SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications. 5331-5335 - Hugo Guterres
, Sang-Jun Park
, Yiwei Cao
, Wonpil Im
:
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site. 5336-5342 - Tiago Sousa
, João Correia
, Vitor Pereira
, Miguel Rocha
:
Generative Deep Learning for Targeted Compound Design. 5343-5361 - Joel Ricci-Lopez
, Sergio A. Aguila, Michael K. Gilson
, Carlos A. Brizuela
:
Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning. 5362-5376 - Pranav Shetty
, Rampi Ramprasad
:
Machine-Guided Polymer Knowledge Extraction Using Natural Language Processing: The Example of Named Entity Normalization. 5377-5385 - Yun Hao
, Jason H. Moore:
TargetTox: A Feature Selection Pipeline for Identifying Predictive Targets Associated with Drug Toxicity. 5386-5394 - Lei Tao, Vikas Varshney
, Ying Li
:
Benchmarking Machine Learning Models for Polymer Informatics: An Example of Glass Transition Temperature. 5395-5413 - Yan Xiang
, Yu-Hang Tang
, Guang Lin
, Huai Sun
:
A Comparative Study of Marginalized Graph Kernel and Message-Passing Neural Network. 5414-5424 - Mingyuan Xu
, Tong Zhu
, John Z. H. Zhang
:
Automated Construction of Neural Network Potential Energy Surface: The Enhanced Self-Organizing Incremental Neural Network Deep Potential Method. 5425-5437 - Carlos H. M. Rodrigues
, Douglas E. V. Pires
, David B. Ascher
:
pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors. 5438-5445 - Miha Gunde
, Nicolas Salles, Anne Hémeryck
, Layla Martin-Samos
:
IRA: A Shape Matching Approach for Recognition and Comparison of Generic Atomic Patterns. 5446-5457 - José-Manuel Gally, Axel Pahl
, Paul Czodrowski
, Herbert Waldmann
:
Pseudonatural Products Occur Frequently in Biologically Relevant Compounds. 5458-5468 - Souvik Banerjee, Shalini Yadav
, Sourav Banerjee, Sayo O. Fakayode, Jyothi Parvathareddy, Walter Reichard, Surekha Surendranathan, Foyez Mahmud, Ryan Whatcott, Joshua Thammathong, Bernd Meibohm, Duane D. Miller, Colleen B. Jonsson, Kshatresh Dutta Dubey:
Drug Repurposing to Identify Nilotinib as a Potential SARS-CoV-2 Main Protease Inhibitor: Insights from a Computational and In Vitro Study. 5469-5483 - Stefano Pantaleone
, Albert Rimola
, Piero Ugliengo
, Mariona Sodupe
:
First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach. 5484-5498 - Felipe J. Valencia
, Max Ramírez, Alejandro Varas, José Rogan
:
Thermal Sensitivity on Eccentric Gold Hollow Nanoparticles: A Perspective from Atomistic Simulations. 5499-5507 - P. Bernát Szabó
, Francesc Sabanés Zariquiey
, Juan J. Nogueira
:
Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations. 5508-5523 - Fatemah Mukadum
, Quan Nguyen, Daniel M. Adrion, Gabriel Appleby, Rui Chen, Haley Dang, Remco Chang, Roman Garnett, Steven A. Lopez
:
Efficient Discovery of Visible Light-Activated Azoarene Photoswitches with Long Half-Lives Using Active Search. 5524-5534 - Yujin Wu, Charles L. Brooks III
:
Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy. 5535-5549 - Dimitrios Kolokouris
, Iris E. Kalenderoglou, Antonios Kolocouris
:
Inside and Out of the Pore: Comparing Interactions and Molecular Dynamics of Influenza A M2 Viroporin Complexes in Standard Lipid Bilayers. 5550-5568 - Carlos Ramírez-Palacios
, Hein J. Wijma
, Sebastian Thallmair
, Siewert J. Marrink
, Dick B. Janssen
:
Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations. 5569-5580 - Mohammed Benabderrahmane, Ronan Bureau
, Anne Sophie Voisin-Chiret
, Jana Sopkova-de Oliveira Santos
:
Cryptic Pockets Repository through Pocket Dynamics Tracking and Metadynamics on Essential Dynamics Space: Applications to Mcl-1. 5581-5588 - Ziqiao Xu, Orrette R. Wauchope, Aaron T. Frank
:
Navigating Chemical Space by Interfacing Generative Artificial Intelligence and Molecular Docking. 5589-5600 - Satoshi Ono
, Matthew R. Naylor
, Chad E. Townsend
, Chieko Okumura, Okimasa Okada
, Hsiau-Wei Lee, R. Scott Lokey
:
Cyclosporin A: Conformational Complexity and Chameleonicity. 5601-5613 - Liang Xu
, Clyde F. Phelix, Liao Y. Chen
:
Structural Insights into the Human Mitochondrial Pyruvate Carrier Complexes. 5614-5625 - Sabahuddin Ahmad
, Christoph Heinrich Strunk, Stephan Schott-Verdugo
, Karl-Erich Jaeger, Filip Kovacic, Holger Gohlke
:
Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity. 5626-5643 - Klaudia Mráziková
, Jirí Sponer
, Vojtech Mlýnský
, Pascal Auffinger
, Holger Kruse
:
Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids. 5644-5657 - Zongfan Yang
, Rebecca M. Twidale, Silvia Gervasoni, Reynier Suardíaz
, Charlotte K. Colenso, Eric J. M. Lang
, James Spencer
, Adrian J. Mulholland
:
Multiscale Workflow for Modeling Ligand Complexes of Zinc Metalloproteins. 5658-5672 - Sayane Shome
, Kannan Sankar, Robert L. Jernigan
:
Simulated Drug Efflux for the AbgT Family of Membrane Transporters. 5673-5681 - Verónica A. Jiménez
:
On the Microtubule-Stabilizing Properties of a Tau Oligopeptide. 5682-5691 - Éva Bertalan
, Elena Lesca, Gebhard F. X. Schertler, Ana-Nicoleta Bondar
:
C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins. 5692-5707 - Avinash Mishra
, Wajihul Hasan Khan
, Anurag S. Rathore
:
Synergistic Effects of Natural Compounds Toward Inhibition of SARS-CoV-2 3CL Protease. 5708-5718 - Lotfi Boudjema, Hanna Aarrass, Marwa Assaf
, Marie Morille
, Gaelle Martin-Gassin
, Pierre-Marie Gassin
:
Correction to "PySHS: Python Open Source Software for Second Harmonic Scattering". 5719 - Mustafa Tekpinar
, Bertrand Néron, Marc Delarue:
Correction to "Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus". 5720
Volume 61, Number 12, December 2021
- Issue Editorial Masthead.
- Issue Publication Information.
- Madison R. Blumer
, Christine H. Chang
, Evangelina Brayfindley
, Jamie R. Nuñez, Sean M. Colby, Ryan S. Renslow
, Thomas O. Metz
:
Mass Spectrometry Adduct Calculator. 5721-5725 - Vincenzo Laveglia, Andrea Giachetti
, Linda Cerofolini, Kevin Haubrich
, Marco Fragai
, Alessio Ciulli
, Antonio Rosato
:
Automated Determination of Nuclear Magnetic Resonance Chemical Shift Perturbations in Ligand Screening Experiments: The PICASSO Web Server. 5726-5733 - Daniel Robert Korn, Vera Pervitsky
, Tesia M. Bobrowski
, Vinicius M. Alves
, Charles Schmitt
, Chris Bizon, Nancy Baker, Rada Chirkova, Artem Cherkasov, Eugene N. Muratov
, Alexander Tropsha
:
COVID-19 Knowledge Extractor (COKE): A Curated Repository of Drug-Target Associations Extracted from the CORD-19 Corpus of Scientific Publications on COVID-19. 5734-5741 - Chanté Muller
, Diane L. Lynch, Dow P. Hurst, Patricia H. Reggio:
TRPV1 Activation by Anandamide via a Unique Lipid Pathway. 5742-5746 - Anjana Puliyanda
, Kaushik Sivaramakrishnan
, Zukui Li
, Arno de Klerk
, Vinay Prasad
:
Structure-Preserving Joint Non-negative Tensor Factorization to Identify Reaction Pathways Using Bayesian Networks. 5747-5762 - Jun Zhao
, Qinhai Ma, Baoyue Zhang, Pengfei Guo, Zhe Wang, Yi Liu, Minsi Meng, Ailin Liu, Zifeng Yang, Guanhua Du:
Exploration of SARS-CoV-2 3CLpro Inhibitors by Virtual Screening Methods, FRET Detection, and CPE Assay. 5763-5773 - Vadim Korolev
, Yuriy M. Nevolin, Thomas A. Manz
, Pavel V. Protsenko
:
Parametrization of Nonbonded Force Field Terms for Metal-Organic Frameworks Using Machine Learning Approach. 5774-5784 - Shunsuke Yuyama
, Hiromasa Kaneko
:
Correlation between the Metal and Organic Components, Structure Property, and Gas-Adsorption Capacity of Metal-Organic Frameworks. 5785-5792 - Jeremy Feinstein, Ganesh Sivaraman
, Kurt Picel, Brian Peters, Álvaro Vázquez-Mayagoitia
, Arvind Ramanathan, Margaret Macdonell, Ian T. Foster, Eugene Yan
:
Uncertainty-Informed Deep Transfer Learning of Perfluoroalkyl and Polyfluoroalkyl Substance Toxicity. 5793-5803 - Hyunseung Kim
, Jonggeol Na
, Won Bo Lee
:
Generative Chemical Transformer: Neural Machine Learning of Molecular Geometric Structures from Chemical Language via Attention. 5804-5814 - Manan Goel, Shampa Raghunathan
, Siddhartha Laghuvarapu
, U. Deva Priyakumar
:
MoleGuLAR: Molecule Generation Using Reinforcement Learning with Alternating Rewards. 5815-5826 - Prosun Halder
, Prerna, Jayant K. Singh
:
Building Unit Extractor for Metal-Organic Frameworks. 5827-5840 - Ilenia Giangreco
, Abhik Mukhopadhyay, Jason C. Cole
:
Validation of a Field-Based Ligand Screener Using a Novel Benchmarking Data Set for Assessing 3D-Based Virtual Screening Methods. 5841-5852 - Gabriel Rath
, Wassja A. Kopp
, Kai Leonhard
:
Coupled Anharmonic Thermochemistry from Stratified Monte Carlo Integration. 5853-5870 - Wen-Hao Deng
, You Lu
, Rong-Zhen Liao
:
Revealing the Mechanism of Isethionate Sulfite-Lyase by QM/MM Calculations. 5871-5882 - Mario Prejanò
, Isabella Romeo, Maria Antonietta La Serra
, Nino Russo
, Tiziana Marino
:
Computational Study Reveals the Role of Water Molecules in the Inhibition Mechanism of LAT1 by 1, 2, 3-Dithiazoles. 5883-5892 - Uta F. Lessel
, Marco Ferrara, Niklas Heine, Chiara Marelli, Laura Carrettoni, Roland Pfau, Esther Schmidt, Doris Riether
:
Identification of Highly Selective Orexin 1 Receptor Antagonists Driven by Structure-Based Design. 5893-5905 - Matthew R. Freidel, Roger S. Armen
:
Modeling the Structure-Activity Relationship of Arbidol Derivatives and Other SARS-CoV-2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein. 5906-5922 - Callum J. Dickson
, Viktor Hornak
, José S. Duca:
Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots. 5923-5930 - Leonid Komissarov
, Toon Verstraelen
:
Improving the Silicon Interactions of GFN-xTB. 5931-5937 - Rafael Maglia de Souza
, Mikko Karttunen
, Mauro Carlos Costa Ribeiro
:
Fine-Tuning the Polarizable CL&Pol Force Field for the Deep Eutectic Solvent Ethaline. 5938-5947 - Ann E. Cleves
, Stephen R. Johnson, Ajay N. Jain
:
Synergy and Complementarity between Focused Machine Learning and Physics-Based Simulation in Affinity Prediction. 5948-5966 - Grigorii V. Andrianov
, Wern Juin Gabriel Ong
, Ilya Serebriiskii, John Karanicolas
:
Efficient Hit-to-Lead Searching of Kinase Inhibitor Chemical Space via Computational Fragment Merging. 5967-5987 - Rebecca M. Twidale
, Philip Hinchliffe
, James Spencer
, Adrian J. Mulholland
:
Crystallography and QM/MM Simulations Identify Preferential Binding of Hydrolyzed Carbapenem and Penem Antibiotics to the L1 Metallo-β-Lactamase in the Imine Form. 5988-5999 - Tomás Bouchal
, Ivo Durník, Petr Kulhánek
:
Bending of Canonical and G/T Mismatched DNAs. 6000-6011 - Jesús San Fabián
, Ignacio Ema, Salama Omar, José Manuel García de la Vega
:
Toward a Computational NMR Procedure for Modeling Dipeptide Side-Chain Conformation. 6012-6023 - Yue Chen, Oliver Fleetwood
, Sergio Pérez-Conesa, Lucie Delemotte
:
Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor. 6024-6037 - Rajarshi Roy
, Nisha Amarnath Jonniya
, Sayan Poddar
, Md Fulbabu Sk
, Parimal Kar
:
Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study. 6038-6052 - Parthiban Marimuthu
, Suresh Gorle
, Konda Reddy Karnati
:
Mechanistic Insights into SARS-CoV-2 Main Protease Inhibition Reveals Hotspot Residues. 6053-6065 - Victor L. Cruz
, Javier Ramos
, Javier Martínez-Salazar, Manuel Montalbán-López, Mercedes Maqueda
:
The Role of Key Amino Acids in the Antimicrobial Mechanism of a Bacteriocin Model Revealed by Molecular Simulations. 6066-6078 - Filip Fratev
:
N501Y and K417N Mutations in the Spike Protein of SARS-CoV-2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study. 6079-6084 - Zhicheng Hu, Lihua Bie
, Jun Gao
, Xiaocong Wang
:
Insights into Selectin Inhibitor Design from Endogenous Isomeric Ligands of SLea and SLex. 6085-6093 - Jaime Rubio-Martinez
, Ana Jiménez-Alesanco
, Laura Ceballos-Laita
, David Ortega-Alarcón
, Sonia Vega
, Cristina Calvo
, Cristina Benítez, Olga Abian
, Adrián Velázquez-Campoy
, Timothy M. Thomson, José Manuel Granadino-Roldán
, Patricia Gómez-Gutiérrez
, Juan Jesús Pérez
:
Discovery of Diverse Natural Products as Inhibitors of SARS-CoV-2 Mpro Protease through Virtual Screening. 6094-6106 - Zhaoxi Sun
, Zhe Huai, Qiao-Le He, Zhirong Liu
:
A General Picture of Cucurbit[8]uril Host-Guest Binding. 6107-6134
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