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ORCIDJournal of Chemical Information and Modeling, Volume 65
Volume 65, Number 1, 2025
- Issue Editorial Masthead.
- Issue Publication Information.
- Valentin Istomin, GiovanniMaria Piccini
:
FESTA: A Polygon-Based Approach for Extracting Relevant Structures from Free Energy Surfaces Obtained in Molecular Simulations. 1-6 - Zheyuan Shen, Rou-fen Chen, Jian Gao, Xinglong Chi, Qing-nan Zhang, Qingyu Bian, Binbin Zhou, Jinxin Che, Haibin Dai, Xiaowu Dong:
EvaluationMaster: A GUI Tool for Structure-Based Virtual Screening Evaluation Analysis and Decision-Making Support. 7-14 - Tagir Akhmetshin, Dmitry V. Zankov, Philippe Gantzer, Dmitry Babadeev, Anna Pinigina, Timur I. Madzhidov, Alexandre Varnek:
SynPlanner: An End-to-End Tool for Synthesis Planning. 15-21 - Danny Reidenbach, Aditi S. Krishnapriyan:
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation. 22-30 - Lei Geng, Yue Feng, Yaxi Niu, Fang Zhang, Huaqing Yin:
MGT: Machine Learning Accelerates Performance Prediction of Alloy Catalytic Materials. 31-40 - Minghui Xin, Zechen Wang, Zhihao Wang, Yuanyuan Qu, Yanmei Yang, Yong-Qiang Li, Ming-Wen Zhao, Liangzhen Zheng, Yuguang Mu, Weifeng Li:
Evaluations of the Perturbation Resistance of the Deep-Learning-Based Ligand Conformation Optimization Algorithm. 41-49 - Jaechan Lee, Dongmin Bang, Sun Kim:
Residue-Level Multiview Deep Learning for ATP Binding Site Prediction and Applications in Kinase Inhibitors. 50-61 - Huazhen Huang, Xianguo Shi, Hongyang Lei, Fan Hu, Yunpeng Cai:
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model. 62-70 - Masami Sako, Nobuaki Yasuo, Masakazu Sekijima:
DiffInt: A Diffusion Model for Structure-Based Drug Design with Explicit Hydrogen Bond Interaction Guidance. 71-82 - Srivathsan Badrinarayanan, Chakradhar Guntuboina, Parisa Mollaei, Amir Barati Farimani:
Multi-Peptide: Multimodality Leveraged Language-Graph Learning of Peptide Properties. 83-91 - Kai-Le Jiang, Huai-Qian Wang, Hui-Fang Li, Shu-Wan Pan, Hao Zheng, Yong-Hang Zhang, Jia-Ming Zhang:
SchNet_IIA: Potential Energy Surface Fitting by Interatomic Interactions Attention Based on Transfer Learning Analysis. 92-100 - Joseph Decorte, Benjamin P. Brown, Rathmell Jeffrey, Jens Meiler:
Interpretable Deep-Learning pKa Prediction for Small Molecule Drugs via Atomic Sensitivity Analysis. 101-113 - Zhihan Liu, Yubo Chai, Jianfeng Li:
Toward Automated Simulation Research Workflow through LLM Prompt Engineering Design. 114-124 - Tuomo Kalliokoski, Ainoleena Turku, Heikki Käsnänen:
SpaceHASTEN: A Structure-Based Virtual Screening Tool for Nonenumerated Virtual Chemical Libraries. 125-132 - Son Gyo Jung, Guwon Jung, Jacqueline M. Cole:
Automatic Prediction of Molecular Properties Using Substructure Vector Embeddings within a Feature Selection Workflow. 133-152 - Maitreyee Sharma Priyadarshini, Nikhil Kumar Thota, Rigoberto Hernandez:
ReLMM: Reinforcement Learning Optimizes Feature Selection in Modeling Materials. 153-161 - Mariia S. Ashikhmina, Artemii Zenkin, Anastasia O. Ivanova, Irina R. Pavlishina, Olga Y. Orlova, Igor Pantiukhin, Ekaterina V. Skorb:
Large Language Model for Automating the Analysis of Cryoprotectants. 162-172 - Dou Nie, Huifeng Zhao, Odin Zhang, Gaoqi Weng, Hui Zhang, Jieyu Jin, Haitao Lin, Yufei Huang, Liwei Liu, Dan Li, Tingjun Hou, Yu Kang:
Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular Generation. 173-186 - Wenjia Qian, Xiaorui Wang, Yuansheng Huang, Yu Kang, Peichen Pan, Chang-Yu Hsieh, Tingjun Hou:
Deep Learning-Driven Insights into Enzyme-Substrate Interaction Discovery. 187-200 - Mario Astigarraga, Andrés Sánchez-Ruiz, Aminata Diop-Aw, Raquel Quintero, Gonzalo Colmenarejo:
How Do Microbial Metabolites Interact with Their Protein Targets? 201-213 - Tianjun Xie, Gerhard R. Wittreich, Matthew T. Curnan, Geun Ho Gu, Kayla N. Seals, Justin S. Tolbert:
Machine-Learning-Enabled Thermochemistry Estimator. 214-222 - Ali Rasouli, Frank C. Pickard, Sreyoshi Sur, Alan Grossfield, Mehtap Isik Bennett:
Essential Considerations for Free Energy Calculations of RNA-Small Molecule Complexes: Lessons from the Theophylline-Binding RNA Aptamer. 223-239 - Marc Domingo, Horacio V. Guzman, Matej Kanduc, Jordi Faraudo:
Electrostatic Interaction between SARS-CoV-2 and Charged Surfaces: Spike Protein Evolution Changed the Game. 240-251 - Bin W. Zhang, Mikolai Fajer, Wei Chen, Francesca Moraca, Lingle Wang:
Leveraging the Thermodynamics of Protein Conformations in Drug Discovery. 252-264 - William Sinko, Blake Mertz, Takafumi Shimizu, Taisuke Takahashi, Yoh Terada, S. Roy Kimura:
ModBind, a Rapid Simulation-Based Predictor of Ligand Binding and Off-Rates. 265-274 - Marco Gibaldi, Anna Kapeliukha, Andrew White, Tom K. Woo:
Incorporation of Ligand Charge and Metal Oxidation State Considerations into the Computational Solvent Removal and Activation of Experimental Crystal Structures Preceding Molecular Simulation. 275-287 - Hyeonjun Kim, Youngshang Pak:
Free Energy-Based Refinement of DNA Force Field via Modification of Multiple Nonbonding Energy Terms. 288-297 - Ayelén Schiel, Rodrigo D. Tosso, Emilio Angelina, Ainhoa García, Nathalie Hennuyer, Diego Cortes, Nuria Cabedo, Ricardo D. Enriz:
N-Tosyl Hydrazone Benzopyran, a New Ligand of PPARα Obtained from Mapping the Conformational Space of Its Active Site. 298-311 - Gufeng Yu, Xi Wang, Yichong Luo, Guanlin Li, Rui Ding, Runhan Shi, Xiaohong Huo, Yang Yang:
Machine Learning for Reaction Performance Prediction in Allylic Substitution Enhanced by Automatic Extraction of a Substrate-Aware Descriptor. 312-325 - Aravind Selvaram Thirunavukarasu, Katarzyna Szleper, Gamze Tanriver, Igor Marchlewski, Karolina Mitusinska, Artur Góra, Jan Brezovsky:
Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model. 326-337 - Melike Berksoz, Canan Atilgan:
Ranking Single Fluorescent Protein-Based Calcium Biosensor Performance by Molecular Dynamics Simulations. 338-350 - Bruno Stegani, Emanuele Scalone, Fran Bacic Toplek, Thomas Löhr, Stefano Gianni, Michele Vendruscolo, Riccardo Capelli, Carlo Camilloni:
Estimation of Ligand Binding Free Energy Using Multi-eGO. 351-362 - William Oliveira Soté, Moacyr Comar Junior:
Exploring Binding Sites in Chagas Disease Protein TcP21 Using Integrated Mixed Solvent Molecular Dynamics Approaches. 363-377 - Tony Eight Lin, Ching-Hsuan Chou, Yi-Wen Wu, Tzu-Ying Sung, Jui-Yi Hsu, Shih-Chung Yen, Jui-Hua Hsieh, Yu-Wei Chang, Shiow-Lin Pan, Wei-Jan Huang, Kai-Cheng Hsu, Chia-Ron Yang:
Identification of a Potent CDK8 Inhibitor Using Structure-Based Virtual Screening. 378-389 - Jiaqi Tian, Wen-Juan Jia, Haibin Dong, Xialin Luo, Lei Gong, Yanxin Ren, Lin Zhong, Jianxun Wang, Danfeng Shi:
Molecular Mechanisms Underlying the Loop-Closing Dynamics of β-1,4 Galactosyltransferase 1. 390-401 - Balázs Krámos, Zoltán Béni, György István Túrós, Olivér Éliás, Attila Potor, Gábor László Kapus, György Szabó:
Ligand Binding and Functional Effect of Novel Bicyclic α5 GABAA Receptor Negative Allosteric Modulators. 402-416 - Nur Afiqah Ahmad, Junming Ho:
Fatty Alcohol Membrane Model for Quantifying and Predicting Amphiphilicity. 417-426 - Rômulo S. Marques, Michael Souza, Fernando Batista, Miguel Gonçalves, Carlile Lavor:
A Probabilistic Approach in the Search Space of the Molecular Distance Geometry Problem. 427-434 - Jing Gu, Tiangang Zhang, Yihang Gao, Sentao Chen, Yuxin Zhang, Hui Cui, Ping Xuan:
Neighborhood Topology-Aware Knowledge Graph Learning and Microbial Preference Inferring for Drug-Microbe Association Prediction. 435-445 - Chen Jiang, Lei Wang, Chang-Qing Yu, Zhu-Hong You, Xin-Fei Wang, Mengmeng Wei, Tai-Long Shi, Si-Zhe Liang, Dengwu Wang:
Hither-CMI: Prediction of circRNA-miRNA Interactions Based on a Hybrid Multimodal Network and Higher-Order Neighborhood Information via a Graph Convolutional Network. 446-459
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