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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
Volume 65, Number 2, 2025
- Qingyu Bian, Zheyuan Shen, Jian Gao, Liteng Shen, Yang Lu, Qing-nan Zhang, Rou-fen Chen, Donghang Xu, Tao Liu, Jinxin Che, Yan Lu, Xiaowu Dong:
PPI-CoAttNet: A Web Server for Protein-Protein Interaction Tasks Using a Coattention Model. 461-471 - Seenivasan Hariharan, Sachin Kinge, Lucas Visscher:
Modeling Heterogeneous Catalysis Using Quantum Computers: An Academic and Industry Perspective. 472-511 - Scott D. Midgley, Sofia Bariami, Matthew Habgood, Mark Mackey:
Adaptive Lambda Scheduling: A Method for Computational Efficiency in Free Energy Perturbation Simulations. 512-516 - Lucas de Almeida Machado, João Sartori, Paula Fernandes da Costa Franklin, Mauricio G. S. Costa, Ana Carolina Ramos Guimarães:
Engineering Protein Dynamics through Mutational Energy Landscape Traps. 517-527 - David Bushiri Pwesombo, Carsten Beese, Christopher Schmied, Han Sun:
Semisupervised Contrastive Learning for Bioactivity Prediction Using Cell Painting Image Data. 528-543 - Bryn Marie Reimer, Ernest Awoonor-Williams, Andrei A. Golosov, Viktor Hornak:
CovCysPredictor: Predicting Selective Covalently Modifiable Cysteines Using Protein Structure and Interpretable Machine Learning. 544-553 - Jie Du, Mingzhi Yuan, Ao Shen, Manning Wang:
PPDock: Pocket Prediction-Based Protein-Ligand Blind Docking. 554-562 - Nisha Kumari, Sonam, Tarak Karmakar:
Enhanced Sampling Simulations of RNA-Peptide Binding Using Deep Learning Collective Variables. 563-570 - Aaron L. Feller, Claus O. Wilke:
Peptide-Aware Chemical Language Model Successfully Predicts Membrane Diffusion of Cyclic Peptides. 571-579 - Yang Yue, Yihua Cheng, Céline Marquet, Chenguang Xiao, Jingjing Guo, Shu Li, Shan He:
Meta-Learning Enables Complex Cluster-Specific Few-Shot Binding Affinity Prediction for Protein-Protein Interactions. 580-588 - Farzin Sohraby, Jing-Yao Guo, Ariane Nunes-Alves:
PathInHydro, a Set of Machine Learning Models to Identify Unbinding Pathways of Gas Molecules in [NiFe] Hydrogenases. 589-602 - Wanxing Li, Xuejing Liu, Yuanfa Liu, Zhaojun Zheng:
High-Accuracy Identification and Structure-Activity Analysis of Antioxidant Peptides via Deep Learning and Quantum Chemistry. 603-612 - Xinhao Qu, Chen Jiang, Mengyi Shan, Wenhao Ke, Jing Chen, Qiming Zhao, Youhong Hu, Jia Liu, Lu-Ping Qin, Gang Cheng:
Prediction of Proteolysis-Targeting Chimeras Retention Time Using XGBoost Model Incorporated with Chromatographic Conditions. 613-625 - Zuolong Zhang, Fang Liu, Xiaonan Shang, Shengbo Chen, Fang Zuo, Yi Wu, Dazhi Long:
ComNet: A Multiview Deep Learning Model for Predicting Drug Combination Side Effects. 626-639 - Kashif Iqbal Sahibzada, Shumaila Shahid, Mohsina Akhter, Rizwan Abid, Muteeba Azhar, Yuansen Hu, Dong-Qing Wei:
HIV OctaScanner: A Machine Learning Approach to Unveil Proteolytic Cleavage Dynamics in HIV-1 Protease Substrates. 640-648 - Bowen Deng, Thijs Stuyver:
Graph-Based Deep Learning Models for Thermodynamic Property Prediction: The Interplay between Target Definition, Data Distribution, Featurization, and Model Architecture. 649-659 - Chuan-Shen Hu, Rishikanta Mayengbam, Kelin Xia, Tze Chien Sum:
Quotient Complex (QC)-Based Machine Learning for 2D Hybrid Perovskite Design. 660-671 - Michael S. Jones, Smayan Khanna, Andrew L. Ferguson:
FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmapping. 672-692 - Vladimir Kozyrev, François Sindt, Didier Rognan:
Active Learning to Select the Most Suitable Reagents and One-Step Organic Chemistry Reactions for Prioritizing Target-Specific Hits from Ultralarge Chemical Spaces. 693-704 - Kairi Furui, Takafumi Shimizu, Yutaka Akiyama, S. Roy Kimura, Yoh Terada, Masahito Ohue:
PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations. 705-721 - Y. Stanley Tan, Mayukh Chakrabarti, Reed M. Stein, Lauren E. Prentis, Robert C. Rizzo, Tom Kurtzman, Marcus Fischer, Trent E. Balius:
Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set. 722-748 - Maria Laura De Sciscio, Fabio Centola, Simona Saporiti, Marco D'Abramo:
Dissecting Methionine Oxidation by Hydrogen Peroxide in Proteins: Thermodynamics, Kinetics, and Susceptibility Descriptors. 749-761 - Jan Choutka, Jakub Kaminský, Ercheng Wang, Kamil Parkan, Radek Pohl:
End-Point Affinity Estimation of Galectin Ligands by Classical and Semiempirical Quantum Mechanical Potentials. 762-777 - Jian Huang, Chenchen Wu, Xiner Yang, Zaixing Yang, Shengtang Liu, Gang Yu:
PACKMOL-GUI: An All-In-One VMD Interface for Efficient Molecular Packing. 778-784 - Hussen O. Mohammed, Abel de Cozar, Ronen Zangi:
Modeling and Elucidating the Behavior of a Thermoresponsive LCST Ionic Liquid. 785-797 - Rui Zhang, Dylan Ye, Anit Gurung, Ralf Warmuth, Daniel G. Kuroda, Lu Wang:
pKa Matching Enables Quantum Proton Delocalization in Acid-1-Methylimidazole Binary Mixtures. 798-810 - Sydney A. Shavalier, J. Daniel Gezelter:
Thermal Transport through CTAB- and MTAB-Functionalized Gold Interfaces Using Molecular Dynamics Simulations. 811-824 - Sahil Kumar, Papiya Dey, Arup Kumar Pathak, Amey Wadawale, Dharmendra K. Maurya, Kalyani Natu, Kakoli Bose, Dibakar Goswami:
Structure-Activity Relationship of Ciprofloxacin towards S-Spike Protein of SARS-CoV-2: Synthesis and In-Silico Evaluation. 825-844 - Mehrnoosh Khodam Hazrati, Lukás Sukeník, Robert Vácha:
Split Membrane: A New Model to Accelerate All-Atom MD Simulation of Phospholipid Bilayers. 845-856 - Fabao Zhao, Liyang Jiang, Jieying Xie, Na Liu, Zhen Gao, Yue Yang, Yu Wang, Boshi Huang, Dongwei Kang, Peng Zhan, Feng Yi, Xinyong Liu:
Discovery of Brain-Penetrative Negative Allosteric Modulators of NMDA Receptors Using FEP-Guided Structure Optimization and Membrane Permeability Prediction. 857-872 - Martin J. Fossat:
MEDOC: A Fast, Scalable, and Mathematically Exact Algorithm for the Site-Specific Prediction of the Protonation Degree in Large Disordered Proteins. 873-881 - Lucas Modesto-Costa, Reed Nieman, Adélia J. A. Aquino, Yehia Mechref, Hans Lischka:
The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times. 882-895 - Toon Lemmens, Jirí Sponer, Miroslav Krepl:
How Binding Site Flexibility Promotes RNA Scanning by TbRGG2 RRM: A Molecular Dynamics Simulation Study. 896-907 - Timothée Rivel, Denys Biriukov, Ivo Kabelka, Robert Vácha:
Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations. 908-920 - Metehan Ilter, Andrés M. Escorcia, Eric Schulze-Niemand, Michael Naumann, Matthias Stein:
Activation and Reactivity of the Deubiquitinylase OTU Cezanne-2 from MD Simulations and QM/MM Calculations. 921-936 - Paige E. Bowling, Dustin R. Broderick, John M. Herbert:
Quick-and-Easy Validation of Protein-Ligand Binding Models Using Fragment-Based Semiempirical Quantum Chemistry. 937-949 - Lei Bao, Wen-Bin Kang, Ben-Chao Zhu, Yi Xiao:
Charge Arrangement Determines the Sensitivity of Aggregation Patterns between Peptide-Chains to the Surrounding Ionic Environment. 950-965 - Yonglan Liu, Wengang Zhang, Hyunbum Jang, Ruth Nussinov:
mTOR Variants Activation Discovers PI3K-like Cryptic Pocket, Expanding Allosteric, Mutant-Selective Inhibitor Designs. 966-980 - Jiahao Xu, Lei Ci, Bo Zhu, Guanhua Zhang, Linhua Jiang, Shixin Ye-Lehmann, Wei Long:
MMSG-DTA: A Multimodal, Multiscale Model Based on Sequence and Graph Modalities for Drug-Target Affinity Prediction. 981-996 - Jun Zhao, Hangcheng Liu, Leyao Kang, Wanling Gao, Quan Lu, Yuan Rao, Zhenyu Yue:
deep-AMPpred: A Deep Learning Method for Identifying Antimicrobial Peptides and Their Functional Activities. 997-1008 - Bei Zhang, Lijun Quan, Zhijun Zhang, Lexin Cao, Qiufeng Chen, Liangchen Peng, Junkai Wang, Yelu Jiang, Liangpeng Nie, Geng Li, Tingfang Wu, Qiang Lyu:
MVCL-DTI: Predicting Drug-Target Interactions Using a Multiview Contrastive Learning Model on a Heterogeneous Graph. 1009-1026 - Jiahui Guan, Danhong Dong, Peilin Xie, Zhihao Zhao, Yilin Guo, Tzong-Yi Lee, Lantian Yao, Ying-Chih Chiang:
StackDILI: Enhancing Drug-Induced Liver Injury Prediction through Stacking Strategy with Effective Molecular Representations. 1027-1039 - Jiashun Wu, Yan Liu, Ying Zhang, Xiaoyu Wang, He Yan, Yiheng Zhu, Jiangning Song, Dong-Jun Yu:
Identifying Protein-Nucleotide Binding Residues via Grouped Multi-task Learning and Pre-trained Protein Language Models. 1040-1052
Volume 65, Number 3, 2025
- Armen G. Beck, Jonathan Fine, Yu-hong Lam, Edward C. Sherer, Erik L. Regalado, Pankaj Aggarwal:
Dedenser: A Python Package for Clustering and Downsampling Chemical Libraries. 1053-1060 - Gonzalo Colmenarejo:
EFGs: A Complete and Accurate Implementation of Ertl's Functional Group Detection Algorithm in RDKit. 1061-1066 - Christian Jorgensen, Raleigh M. Linville, Ian Galea, Edward Lambden, Martin Vögele, Charles Chen, Evan P. Troendle, Fiorella Ruggiu, Martin B. Ulmschneider, Birgit Schiøtt, Christian D. Lorenz:
Permeability Benchmarking: Guidelines for Comparing in Silico, in Vitro, and in Vivo Measurements. 1067-1084 - Guangying Jin, Wei Ran, Manyue Zhang, Yun Li:
An Intelligent Prediction Model for the Synthesis Conditions of Metal-Organic Frameworks Utilizing Artificial Neural Networks Enhanced by Genetic Algorithm Optimization. 1085-1100 - Song Xia, Yaowen Gu, Yingkai Zhang:
Normalized Protein-Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening. 1101-1114 - Jinyong Park, Minhi Han, Kiwoong Lee, Sungnam Park:
Hierarchical Graph Attention Network with Positive and Negative Attentions for Improved Interpretability: ISA-PN. 1115-1127 - Nandan Kumar, Zhenjiao Du, Yonghui Li:
pLM4CPPs: Protein Language Model-Based Predictor for Cell Penetrating Peptides. 1128-1139 - Zhe Zhang, Ruyu Gao, Meiling Zhao, Xiangying Zhang, Haotian Gao, Yifei Qi, Renxiao Wang, Yan Li:
Computational Methods for Predicting Chemical Reactivity of Covalent Compounds. 1140-1154 - Xinqi Li, Ryan Walsh, Waseem Abbas, Sergio Pascual-Diaz, Calum Hand, Rory Garland, Faiz Mohammad Khan, Nikhil Mohan Das, Vedant Desai, Mohamed Abouzleikha, Matthew A. Clark:
Multiclass Synthetic Accessibility Prediction. 1155-1165 - Xinyue Ma, Fenglei Li, Qianyu Chen, Shenghua Gao, Fang Bai:
NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface. 1166-1177 - Nianze Tao, Minori Abe:
Bayesian Flow Network Framework for Chemistry Tasks. 1178-1187 - Shan Lu, Nicholas J. Huls, Koushiki Basu, Tonglei Li:
Deep Learning of CYP450 Binding of Small Molecules by Quantum Information. 1188-1197 - Luan G. F. dos Santos, Benjamin T. Nebgen, Alice E. A. Allen, Brenden W. Hamilton, Sakib Matin, Justin S. Smith, Richard A. Messerly:
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation. 1198-1210 - Yongna Yuan, Siming Chen, Rizhen Hu, Xin Wang:
MutualDTA: An Interpretable Drug-Target Affinity Prediction Model Leveraging Pretrained Models and Mutual Attention. 1211-1227 - Mohammadamin Tavakoli, Yin Ting T. Chiu, Ann Marie Carlton, David Van Vranken, Pierre Baldi:
Chemically Informed Deep Learning for Interpretable Radical Reaction Prediction. 1228-1242 - Connor O'ryan, Kevin D. Hayes, Francis G. VanGessel, Ruth M. Doherty, William Wilson, John Fischer, Zois Boukouvalas, Peter W. Chung:
An Automated Approach for Domain-Specific Knowledge Graph Generation─Graph Measures and Characterization. 1243-1257 - Teresa Maria Creanza, Domenico Alberga, Cosimo Patruno, Giuseppe Felice Mangiatordi, Nicola Ancona:
Transformer Decoder Learns from a Pretrained Protein Language Model to Generate Ligands with High Affinity. 1258-1277 - Elizaveta Mukhaleva, Babgen Manookian, Hanyu Chen, Indira R. Sivaraj, Ning Ma, Wenyuan Wei, Konstancja Urbaniak, Grigoriy Gogoshin, Supriyo Bhattacharya, Nagarajan Vaidehi, Andrei S. Rodin, Sergio Branciamore:
BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories. 1278-1288 - João G. Neto, Karla Figueiredo, João B. P. Soares, Amanda L. T. Brandão:
Can Focusing on One Deep Learning Architecture Improve Fault Diagnosis Performance? 1289-1304 - Huynh Anh Duy, Tarapong Srisongkram:
Comparative Analysis of Recurrent Neural Networks with Conjoint Fingerprints for Skin Corrosion Prediction. 1305-1317 - Lihong Peng, Jiale Mao, Guohua Huang, Guosheng Han, Xin Liu, Wen Liao, Geng Tian, Jialiang Yang:
DO-GMA: An End-to-End Drug-Target Interaction Identification Framework with a Depthwise Overparameterized Convolutional Network and the Gated Multihead Attention Mechanism. 1318-1337 - Sourav Pal, Kellie D. Nance, Dirgha Raj Joshi, Stephen C. Kales, Lin Ye, Xin Hu, Khalida Shamim, Alexey V. Zakharov:
Applications of Machine Learning Approaches for the Discovery of SARS-CoV-2 PLpro Inhibitors. 1338-1356 - Alec Lamens, Jürgen Bajorath:
Rationalizing Predictions of Isoform-Selective Phosphoinositide 3-Kinase Inhibitors Using MolAnchor Analysis. 1357-1366 - Han-Chung Chang, Ming-Hsuan Tsai, Yi-Pei Li:
Enhancing Activation Energy Predictions under Data Constraints Using Graph Neural Networks. 1367-1377 - Roberta Astolfi, Alessandra Oliva, Antonio Raffo, Filippo Sapienza, Alessio Ragno, Eleonora Proia, Claudio M. Mastroianni, Cristina Luceri, Mijat Bozovic, Milan Mladenovic, Rosanna Papa, Patrizia Bottoni, Elena Mazzinelli, Giuseppina Nocca, Rino Ragno:
Essential Oils as Antimicrobials against Acinetobacter baumannii: Experimental and Literature Data to Definite Predictive Quantitative Composition-Activity Relationship Models Using Machine Learning Algorithms. 1378-1391 - Ara M. Abramyan, Anna Bochicchio, Chuanjie Wu, Wolfgang Damm, David R. Langley, Devleena Shivakumar, Dmitry Lupyan, Lingle Wang, Edward Harder, Eliud O. Oloo:
Accurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands. 1392-1403 - Laura Scalvini, Daniele Pala, Alberto Cuzzolin, Francesca Galvani, Alessio Lodola, Silvia Rivara, Marco Mor, Andrea Rizzi:
JAK3 Inhibitors: Covalent and Noncovalent Interactions of a Cyanamide Group Investigated by Multiscale Free-Energy Simulations. 1404-1418 - Guangbin Cheng, Bingyi Wang, Nannan Bai, Weihua Li:
ABCoRT: Retention Time Prediction for Metabolite Identification via Atom-Bond Co-Learning. 1419-1427 - Yong Duan, Junmei Wang, Piotr Cieplak, Ray Luo:
Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials. 1428-1440 - Andrea Dodaro, Gianluca Novello, Silvia Menin, Chiara Cavastracci Strascia, Mattia Sturlese, Veronica Salmaso, Stefano Moro:
Post-Docking Refinement of Peptide or Protein-RNA Complexes Using Thermal Titration Molecular Dynamics (TTMD): A Stability Insight. 1441-1452 - Golbarg Gazerani, Lesley R. Piercey, Syeda Reema, Katie A. Wilson:
Examining the Biophysical Properties of the Inner Membrane of Gram-Negative ESKAPE Pathogens. 1453-1464 - David A. Cooper, Joseph Depaolo-Boisvert, Stanley A. Nicholson, Barien Gad, David D. L. Minh:
Intracellular Pocket Conformations Determine Signaling Efficacy through the μ Opioid Receptor. 1465-1475 - Mariia Savenko, Robert Vácha, Christophe Ramseyer, Timothée Rivel:
Role of Divalent Ions in Membrane Models of Polymyxin-Sensitive and Resistant Gram-Negative Bacteria. 1476-1491 - Matteo Pavan, Silvia Menin, Andrea Dodaro, Gianluca Novello, Chiara Cavastracci Strascia, Mattia Sturlese, Veronica Salmaso, Stefano Moro:
Thermal Titration Molecular Dynamics: The Revenge of the Fragments. 1492-1513 - Hongyu Xu, Tong Li, Qi Wang, Yang Lv, Changhong Sun, Rui Yan, Xiaodan Wu, Yingxue Jin, Zhiqiang Wang:
Small Molecular Oligopeptides Adorned with Tryptophan Residues as Potent Antitumor Agents: Design, Synthesis, Bioactivity Assay, Computational Prediction, and Experimental Validation. 1514-1536 - Astrid F. Brandner, Iain Peter Shand Smith, Siewert J. Marrink, Paulo C. T. Souza, Syma Khalid:
Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field. 1537-1548 - Eric Catalina-Hernandez, Marcel Aguilella-Arzo, Alex Perálvarez-Marín, Mario Lopez-Martin:
Computational Insights into Membrane Disruption by Cell-Penetrating Peptides. 1549-1559 - Hervé Hogues, Wanlei Wei, Traian Sulea:
Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design. 1560-1569 - Sathish Dasari, Subha Kalyaanamoorthy:
Impact of Phosphorylation and O-GlcNAcylation on the Binding Affinity of R4 Tau Peptide to Microtubule and Its Conformational Preference upon Dissociation. 1570-1584 - Ryan Dykstra, Dan Sindhikara:
Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics. 1585-1604 - K. Harini, Masakazu Sekijima, M. Michael Gromiha:
PRA-MutPred: Predicting the Effect of Point Mutations in Protein-RNA Complexes Using Structural Features. 1605-1614 - Guishen Wang, Hangchen Zhang, Mengting Shao, Shisen Sun, Chen Cao:
MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction. 1615-1630 - Ping Xuan, Xiaoying Qi, Sentao Chen, Jing Gu, Xiuju Wang, Hui Cui, Jun Lu, Tiangang Zhang:
Subgraph Topology and Dynamic Graph Topology Enhanced Graph Learning and Pairwise Feature Context Relationship Integration for Predicting Disease-Related miRNAs. 1631-1640 - Hong Cao, Jiahua He, Tao Li, Sheng-You Huang:
Deciphering Protein Secondary Structures and Nucleic Acids in Cryo-EM Maps Using Deep Learning. 1641-1652 - Yuanyuan Zhang, Haoyu Zheng, Xiaokun Meng, Qihao Wang, Zimin Li, Wenhao Wu:
MOCapsNet: Multiomics Data Integration for Cancer Subtype Analysis Based on Dynamic Self-Attention Learning and Capsule Networks. 1653-1665 - Si-Zhe Liang, Lei Wang, Zhu-Hong You, Chang-Qing Yu, Mengmeng Wei, Yu Wei, Tai-Long Shi, Chen Jiang:
Predicting circRNA-Disease Associations through Multisource Domain-Aware Embeddings and Feature Projection Networks. 1666-1676
Volume 65, Number 4, 2025
- Sergio Pantano, Luciana Capece, Laura Gagliardi, Kenneth M. Merz Jr., Victor S. Batista, Thereza A. Soares:
Computational Chemistry in the Global South: A Latin American Perspective. 1677-1678 - Raquel Lopez-Rios de Castro, Alejandro Santana-Bonilla, Robert M. Ziolek, Christian D. Lorenz:
Automated Analysis of Soft Matter Interfaces, Interactions, and Self-Assembly with PySoftK. 1679-1684 - Jokent T. Gaza, Emiliano Brini, Justin L. Maccallum, Ken A. Dill, Alberto Pérez:
MELD in Action: Harnessing Data to Accelerate Molecular Dynamics. 1685-1693 - Hrachya Ishkhanyan, Alejandro Santana-Bonilla, Christian D. Lorenz:
PUCHIK: A Python Package To Analyze Molecular Dynamics Simulations of Aspherical Nanoparticles. 1694-1701 - Søren Bertelsen, Sigurd Carlsen, Søren Furbo, Morten Bormann Nielsen, Aksel Obdrup, Rolf Taaning:
ProcessOptimizer, an Open-Source Python Package for Easy Optimization of Real-World Processes Using Bayesian Optimization: Showcase of Features and Example of Use. 1702-1707 - Xiangrun Zhou, Guixia Liu, Shuyuan Cao, Ji Lv:
Deep Learning for Antimicrobial Peptides: Computational Models and Databases. 1708-1717 - Elizaveta I. Yakovenko, Iurii M. Nevolin, Anatoliy A. Chasovskikh, Artem A. Mitrofanov, Vadim V. Korolev:
Data-Driven Prediction of Structures of Metal-Organic Frameworks. 1718-1723 - Yunjiang Zhang, Chenyu Huang, Yaxin Wang, Shuyuan Li, Shaorui Sun:
CL-GNN: Contrastive Learning and Graph Neural Network for Protein-Ligand Binding Affinity Prediction. 1724-1735 - Kirti Sharma, Pawan K. Tiwari, S. K. Sinha:
Estimation of Hematocrit Volume Using Blood Glucose Concentration through Extreme Gradient Boosting Regressor Machine Learning Model. 1736-1746 - Giovanni Trezza, Eliodoro Chiavazzo:
Classification-Based Detection and Quantification of Cross-Domain Data Bias in Materials Discovery. 1747-1761 - Edvin Forsgren, Benny Björkblom, Johan Trygg, Pär Jonsson:
OPLS-Based Multiclass Classification and Data-Driven Interclass Relationship Discovery. 1762-1770 - Peter B. R. Hartog, Annie M. Westerlund, Igor V. Tetko, Samuel Genheden:
Investigations into the Efficiency of Computer-Aided Synthesis Planning. 1771-1781 - Floriane Eshak, Anne Goupil-Lamy:
Advancements in Nanobody Epitope Prediction: A Comparative Study of AlphaFold2Multimer vs AlphaFold3. 1782-1797 - André Brasil Vieira Wyzykowski, Fatemeh Fathi Niazi, Alex Dickson:
AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction. 1798-1811 - Luis E. Castro-Anaya, Eduardo Marese, Jaime A. Lozano, Guilherme F. Peixer, Jader R. Barbosa, Sergio Yesid Gómez González:
Machine Learning Methodologies Applied to Magnetocaloric Perovskites Discovery. 1812-1825 - Alexandria Van Grouw, Markace A. Rainey, Olivia K. Reid, Molly M. Ogle, Samuel G. Moore, Johnna S. Temenoff, Facundo M. Fernández:
Toward Machine Learning Electrospray Ionization Sensitivity Prediction for Semiquantitative Lipidomics in Stem Cells. 1826-1836 - Tiffani Hui, Maxim Secor, Minh Ngoc Ho, Nomindari Bayaraa, Yu-Shan Lin:
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids. 1837-1849 - Fabrizio Mastrolorito, Nicola Gambacorta, Fulvio Ciriaco, F. Cutropia, Maria Vittoria Togo, V. Belgiovine, Anna Rita Tondo, D. Trisciuzzi, A. Monaco, R. Bellotti, Cosimo Damiano Altomare, Orazio Nicolotti, N. Amoroso:
Chemical Space Networks Enhance Toxicity Recognition via Graph Embedding. 1850-1861 - Kerrin Janssen, Jonny Proppe:
Predicting and Explaining Yields with Machine Learning for Carboxylated Azoles and Beyond. 1862-1872 - Pankaj Kumar, Saurabh Kabra, Jacqueline M. Cole:
MechBERT: Language Models for Extracting Chemical and Property Relationships about Mechanical Stress and Strain. 1873-1888 - Leandro Martínez Heredia, Patricia A. Quispe, Julián F. Fernández, Martin J. Lavecchia:
NaturAr: A Collaborative, Open-Source Database of Natural Products from Argentinian Biodiversity for Drug Discovery and Bioprospecting. 1889-1900 - Mohammad Ali, Yuta Mizuno, Seiji Akiyama, Yuuya Nagata, Tamiki Komatsuzaki:
Enumeration Approach to Atom-to-Atom Mapping Accelerated by Ising Computing. 1901-1910 - Victor H. R. Nogueira, Rishabh Sharma, Rafael V. C. Guido, Michael J. Keiser:
Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation. 1911-1927 - Fuqiang Chen, Chenghua Zhang, Shiqing Zhang, Wuyuan Zhang, Hao Su, Xiang Sheng:
Computational Modeling of the Enzymatic Achmatowicz Rearrangement by Heme-Dependent Chloroperoxidase: Reaction Mechanism, Enantiopreference, Regioselectivity, and Substrate Specificity. 1928-1939 - Jiwon Seo, Ravi Singh, Jun-Ho Choi:
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions. 1940-1952 - Bin Chen, Tian-Tian Feng, Da-Gang Zhou, Li-Jun Yang:
Mechanisms of C(sp3)-H Functionalization of Acetonitrile or Acetone with Alkynes: A DFT Investigation. 1953-1966 - Valerij Talagayev, Yu Chen, Niklas Piet Doering, Leon Obendorf, Katrin Denzinger, Kristina Puls, Kevin Lam, Sijie Liu, Clemens Alexander Wolf, Theresa Noonan, Marko Breznik, Petra Knaus, Gerhard Wolber:
OpenMMDL - Simplifying the Complex: Building, Simulating, and Analyzing Protein-Ligand Systems in OpenMM. 1967-1978 - Yixin Luo, Dongsheng Chen, Chen Zhang, Jinkun Yang, Tian Gao, Xiaojing Luo:
Simulation of Interface Characteristics and Charge Transfer Dynamics for Layered Electrodes Using Cascade Capacitance in Supercapacitors by COMSOL Software. 1979-1989 - Yahui Cao, Tao Zhang, Xin Zhao, Haotong Li:
HiRXN: Hierarchical Attention-Based Representation Learning for Chemical Reaction. 1990-2002 - Alexander Zlobin, Valentina D. Maslova, Julia Beliaeva, Jens Meiler, Andrey V. Golovin:
Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design. 2003-2013 - Cuiyu Li, Hongyan Du, Chengwei Zhang, Wanying Huang, Xujun Zhang, Tianyue Wang, Dejun Jiang, Tingjun Hou, Ercheng Wang:
Comprehensive Evaluation of End-Point Free Energy Methods in DNA-Ligand Interaction Predictions. 2014-2025 - Binbin Chen, Jiahui Huang, Yingchun Liu, Lirong Yang, Qi Wang, Haoran Yu:
Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids. 2026-2037 - Pedro A. Valiente, Yasel Guerra, Maarten G. Wolf, Isel Pascual, Enrique Rudiño-Piñera, Isabelle Florent, Tirso Pons, Gerrit Groenhof:
Discovery of a Noncompetitive Open-Flap Selective Inhibitor of Plasmepsin II with Antiplasmodial Activity. 2038-2051 - Andrea Basciu, Mohd Athar, Han Kurt, Christine Neville, Giuliano Malloci, Fabrizio C. Muredda, Andrea Bosin, Paolo Ruggerone, Alexandre M. J. J. Bonvin, Attilio Vittorio Vargiu:
Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins. 2052-2065 - Lulu Guan, Bote Qi, Jingwang Tan, Yukang Chen, Yunxiang Sun, Qingwen Zhang, Yu Zou:
Structural Insight into the Inactive/Active States of 5-HT1AR and Molecular Mechanisms of Electric Fields in Modulating 5-HT1AR. 2066-2079 - Honghui Zhang, Hajime Hirao:
Mechanism of Regio- and Enantioselective Hydroxylation of Arachidonic Acid Catalyzed by Human CYP2E1: A Combined Molecular Dynamics and Quantum Mechanics/Molecular Mechanics Study. 2080-2092 - Sezer Sorgun, Kahraman Birgin:
Vertex-Edge-Weighted Molecular Graphs: A Study on Topological Indices and Their Relevance to Physicochemical Properties of Drugs Used in Cancer Treatment. 2093-2106 - Meiting Wang, Hao Jiang, Ulf Ryde:
Impact of Varying Velocities and Solvation Boxes on Alchemical Free-Energy Simulations. 2107-2115 - Stephane Jedele, Benoit Allegrini, Hélène Guizouarn, Catherine Etchebest:
Investigating the Dynamics of the KCNN4 Channel: From the Determination of the Complete K+ Permeation Pathway Across the Channel to Its Opening by PIP2. 2116-2128 - Li Peng, Huaping Li, Sisi Yuan, Tao Meng, Yifan Chen, Xiangzheng Fu, Dongsheng Cao:
metaCDA: A Novel Framework for CircRNA-Driven Drug Discovery Utilizing Adaptive Aggregation and Meta-Knowledge Learning. 2129-2144 - Yan-Yun Chang, Yu-Chen Liu, Wei-En Jhang, Sin-Siang Wei, Yu-Yen Ou:
CaBind_MCNN: Identifying Potential Calcium Channel Blocker Targets by Predicting Calcium-Binding Sites in Ion Channels and Ion Transporters Using Protein Language Models and Multiscale Feature Extraction. 2145-2157 - Tiyao Liu, Shudong Wang, Shanchen Pang, Xiaodong Tan:
Truncated Arctangent Rank Minimization and Double-Strategy Neighborhood Constraint Graph Inference for Drug-Disease Association Prediction. 2158-2172
Volume 65, Number 5, 2025
- Mengmeng Liu, Xialong Ni, J. Ramanujam, Michal Brylinski:
EC2Vec: A Machine Learning Method to Embed Enzyme Commission (EC) Numbers into Vector Representations. 2173-2179 - Christian Kramer, John D. Chodera, Kelly L. Damm-Ganamet, Michael K. Gilson, Judith Guenther, Uta F. Lessel, Richard A. Lewis, David L. Mobley, Eva Nittinger, Adam Pecina, Matthieu Schapira, W. Patrick Walters:
The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks. 2180-2190 - James Michels, Ramya Bandarupalli, Amin Ahangar Akbari, Thai Le, Hong Xiao, Jing Li, Erik F. Y. Hom:
Natural Language Processing Methods for the Study of Protein-Ligand Interactions. 2191-2213 - Amit Gangwal, Antonio Lavecchia:
AI-Driven Drug Discovery for Rare Diseases. 2214-2231 - Junlin Xu, Xiaobo Wen, Li Sun, Kunyue Xing, Linyuan Xue, Sha Zhou, Jiayi Hu, Zhijuan Ai, Qian Kong, Zishu Wen, Li Guo, Minglu Hao, Dongming Xing:
Large Model Era: Deep Learning in Osteoporosis Drug Discovery. 2232-2244 - Yusuke Tanabe, Hiroki Sugisawa, Tomohisa Miyazawa, Kazuhiro Hotta, Kazuya Shiratori, Tadahiro Fujitani:
High-Throughput Optimization of a High-Pressure Catalytic Reaction. 2245-2250 - Hongtao Zhao, Karolina Kwapien, Eva Nittinger, Christian Tyrchan, Magnus Nilsson, Susanne Berglund, Werngard Czechtizky:
AI-Augmented R-Group Exploration in Medicinal Chemistry. 2251-2255 - Zidong Su, Rong Zhang, Xiaoyu Fan, Boxue Tian:
SynthMol: A Drug Safety Prediction Framework Integrating Graph Attention and Molecular Descriptors into Pre-Trained Geometric Models. 2256-2267 - Hengzheng Yang, Jian Xiu, Weiqi Yan, Kaifeng Liu, Huizi Cui, Zhibang Wang, Qizheng He, Yilin Gao, Weiwei Han:
Large Language Models as Tools for Molecular Toxicity Prediction: AI Insights into Cardiotoxicity. 2268-2282 - Jinyeong Park, Jaegyoon Ahn, Jonghwan Choi, Jibum Kim:
Mol-AIR: Molecular Reinforcement Learning with Adaptive Intrinsic Rewards for Goal-Directed Molecular Generation. 2283-2296 - Bowen Li, Jin Xiao, Ya Gao, John Z. H. Zhang, Tong Zhu:
Transition State Searching Accelerated by Neural Network Potential. 2297-2303 - Feixiang Zhou, Shuo Zhang, Huifeng Zhang, Jian K. Liu:
ProCeSa: Contrast-Enhanced Structure-Aware Network for Thermostability Prediction with Protein Language Models. 2304-2313 - Thomas Hehre, Philip E. Klunzinger, Bernard Deppmeier, William Ohlinger, Warren Hehre:
Accurate Prediction of ωB97X-D/6-31G* Equilibrium Geometries from a Neural Net Starting from Merck Molecular Force Field (MMFF) Molecular Mechanics Geometries. 2314-2321 - Xuhai Huang, Jiamin Chang, Boxue Tian:
GLMCyp: A Deep Learning-Based Method for CYP450-Mediated Reaction Site Prediction. 2322-2335 - Aoyun Geng, Zhenjie Luo, Aohan Li, Zilong Zhang, Quan Zou, Leyi Wei, Feifei Cui:
ACP-CLB: An Anticancer Peptide Prediction Model Based on Multichannel Discriminative Processing and Integration of Large Pretrained Protein Language Models. 2336-2349 - Xiayi Zhao, Bao Wang, Kun Zhou, Jiangjiexing Wu, Kai Song:
High-Throughput Prediction of Metal-Embedded Complex Properties with a New GNN-Based Metal Attention Framework. 2350-2360 - Rogerio Margis, Iara Macedo, Nureyev F. Rodrigues, Mateus Dias-Oliveira, Fernanda Lazzarotto, Diego Trindade de Souza, Geancarlo Zanatta:
NABhClassifier Server: A Tool for the Identification of Helical Nucleic Acid-Binding Sequences in Proteins. 2361-2367 - Youxu Dai, Aiping Han, Hui-Jun Ma, Xuebo Jin, Danyang Zhu, Shiguang Sun, Ruiheng Li:
Binding Affinity Prediction and Pesticide Screening against Phytophthora sojae Using a Heterogeneous Interaction Graph Attention Network-Based Model. 2368-2384 - Cailum M. K. Stienstra, Teun van Wieringen, Liam Hebert, Patrick Thomas, Kas J. Houthuijs, Giel Berden, Jos Oomens, Jonathan Martens, W. Scott Hopkins:
A Machine-Learned "Chemical Intuition" to Overcome Spectroscopic Data Scarcity. 2385-2394 - Gregory W. Kyro, Anthony M. Smaldone, Yu Shee, Chuzhi Xu, Victor S. Batista:
T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction with Uncertainty-Aware Self-Learning for Protein-Specific Alignment. 2395-2415 - Yojana Gadiya, Olga Genilloud, Ursula Bilitewski, Mark Brönstrup, Leonie von Berlin, Marie Attwood, Philip Gribbon, Andrea Zaliani:
Predicting Antimicrobial Class Specificity of Small Molecules Using Machine Learning. 2416-2431 - Yunyin Li, Shudong Wang, Yuanyuan Zhang, Chuanru Ren, Tiyao Liu, Yingye Liu, Shanchen Pang:
IRPCA: An Interpretable Robust Principal Component Analysis Framework for Inferring miRNA-Drug Associations. 2432-2442 - Andreas Vitalis, Steffen Winkler, Yang Zhang, Julian Widmer, Amedeo Caflisch:
A FAIR-Compliant Management Solution for Molecular Simulation Trajectories. 2443-2455 - Christian Fellinger, Thomas Seidel, Benjamin Merget, Klaus-Jürgen Schleifer, Thierry Langer:
GRADE and X-GRADE: Unveiling Novel Protein-Ligand Interaction Fingerprints Based on GRAIL Scores. 2456-2475 - DingYun Huang, Jacqueline M. Cole:
Cost-Efficient Domain-Adaptive Pretraining of Language Models for Optoelectronics Applications. 2476-2486 - Talant Ruzmetov, Ta I Hung, Saisri Padmaja Jonnalagedda, Si-Han Chen, Parisa Fasihianifard, Zhefeng Guo, Bir Bhanu, Chia-en A. Chang:
Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning. 2487-2502 - Peter Mastracco, Luke Nambi Mohanam, Giacomo Nagaro, Sangram Prusty, Younghoon Oh, Ruqian Wu, Qiang Cui, Allon I. Hochbaum, Stacy M. Copp, Sahar Sharifzadeh:
Dynamic Electronic Structure Fluctuations in the De Novo Peptide ACC-Dimer Revealed by First-Principles Theory and Machine Learning. 2503-2512 - Yifan Wang, Lorenz Fleitmann, Lukas Raßpe-Lange, Niklas von der Aßen, André Bardow, Kai Leonhard:
Fine-Tuning a Genetic Algorithm for CAMD: A Screening-Guided Warm Start. 2513-2529 - Ali Ebrahimpoor Gorji, Juho-Pekka Laakso, Ville Alopaeus, Petri Uusi-Kyyny:
MLR Data-Driven for the Prediction of Infinite Dilution Activity Coefficient of Water in Ionic Liquids (ILs) Using QSPR-Based COSMO Descriptors. 2530-2542 - Anu Nagarajan, Katherine Amberg-Johnson, Evan Paull, Kunling Huang, Phani Ghanakota, Asela Chandrasinghe, Jackson Chief Elk, Jared M. Sampson, Lingle Wang, Robert Abel, Steven K. Albanese:
Predicting Resistance to Small Molecule Kinase Inhibitors. 2543-2557 - Mayank Shriwastav, Abhishek Kumar Gupta, D. K. Dwivedi:
Computational Investigation of Site-Specific Doping Effects on Electronic Structure, Electrochemical Performance, Lithium-Ion Diffusion, and Transport in Li2GeO3 Anode. 2558-2571 - Haipeng Wang, Xuyang Liu, Wensheng Cai, Xueguang Shao:
Head-to-Tail Cyclization Enhances Ice-Growth Inhibition by Linear Threonine Oligomers. 2572-2591 - Fangjian Shang, Huaxin Liu, Jianyong Liu, Meiheng Lv, Yinhua Ma:
Theoretical Study on the Key Influence of Ionic Liquid on the Synthesis Method of HMX by DPT. 2592-2601 - Elton José Ferreira Chaves, João Sartori, Whendel M. Santos, Carlos H. B. Cruz, Emmanuel N. Mhrous, Manassés F. Nacimento-Filho, Matheus Vitor Ferreira Ferraz, Roberto D. Lins:
Estimating Absolute Protein-Protein Binding Free Energies by a Super Learner Model. 2602-2609 - Jingyuan Zhuang, Wei Yang, Gui-Juan Cheng:
Mechanistic Insights into the Reversible Inhibition of d-Cycloserine in Alanine Racemase from Mycobacterium tuberculosis. 2610-2622 - Lei Liu, Zhihong Shi, Mingqiong Tong, Yaqing Fang, Dongying Yang, Jiafeng Yu, Zanxia Cao:
Designing a Novel Ultrashort Cyclic [R3W4V] Antimicrobial Peptide with Superior Antimicrobial Potential Based on the Transmembrane Structure to Facilitate Pore Formation. 2623-2635 - Vinícius Alexandre Fiaia Costa, Flávia Nader Motta, Alexandra Maria dos Santos Carvalho, Felipe da Silva Mendonça de Melo, Melina Mottin, Sébastien Charneau, Philippe Grellier, Jaime Martins Santana, Izabela Marques Dourado Bastos, Bruno Junior Neves:
Structure-Based Identification of Non-covalent Prolyl Oligopeptidase 80 Inhibitors Targeting Trypanosoma cruzi Cell Entry. 2636-2649 - Bruno Di Geronimo, Spela Mandl, Santiago Alonso-Gil, Bojan Zagrovic, Gilbert Reibnegger, Christoph Nusshold, Pedro A. Sánchez-Murcia:
Digging out the Molecular Connections between the Catalytic Mechanism of Human Lysosomal α-Mannosidase and Its Pathophysiology. 2650-2659 - Guilherme Menegon Arantes:
Redox-Activated Proton Transfer through a Redundant Network in the Qo Site of Cytochrome bc1. 2660-2669 - Yi Zhang, Yin Wang, Xinyuan Liu, Xi Feng:
PbImpute: Precise Zero Discrimination and Balanced Imputation in Single-Cell RNA Sequencing Data. 2670-2684 - Cheng-Che Chuang, Yu-Chen Liu, Wei-En Jhang, Sin-Siang Wei, Yu-Yen Ou:
RAG_MCNNIL6: A Retrieval-Augmented Multi-Window Convolutional Network for Accurate Prediction of IL-6 Inducing Epitopes. 2685-2694 - Greta Grassmann, Lorenzo Di Rienzo, Giancarlo Ruocco, Mattia Miotto, Edoardo Milanetti:
Compact Assessment of Molecular Surface Complementarities Enhances Neural Network-Aided Prediction of Key Binding Residues. 2695-2709 - Shiji Zhao, Andrew J. Schaub, Shiou-Chuan Tsai, Ray Luo:
Correction to "Development of a Pantetheine Force Field Library for Molecular Modeling". 2710
Volume 65, Number 6, 2025
- Pengfei Li, Tingting Pu, Ye Mei:
FEP-SPell-ABFE: An Open-Source Automated Alchemical Absolute Binding Free-Energy Calculation Workflow for Drug Discovery. 2711-2721 - Yu-Hong Liu, Hong-Quan Xu, Si-Si Zhu, Yan-Feng Hong, Xiu-Wen Li, Hong-Xiu Li, Jun-Peng Xiong, Huan Xiao, Jin-Hui Bu, Feng Zhu, Lin Tao:
ASVirus: A Comprehensive Knowledgebase for the Viral Alternative Splicing. 2722-2729 - José Adriano da Silva, Paulo Augusto Netz, Mario Roberto Meneghetti:
Applying Molecular Dynamics Simulations to Unveil the Anisotropic Growth Mechanism of Gold Nanorods: Advances and Perspectives. 2730-2740 - Chuan-qi Sun, Zhi-min Li, Yu Ji, Ulrich Schwaneberg, Zong-lin Li:
CMDmpnn: Combining Comparative Molecular Dynamics and ProteinMPNN to Rapidly Expand Enzyme Substrate Spectrum. 2741-2747 - So Eun Choi, Miyoung Jang, Sohee Yoon, Sanghyun Yoo, Jooyeon Ahn, Minho Kim, Ho-Gyeong Kim, Yebin Jung, Seongeon Park, Young-Seok Kim, Taekhoon Kim:
LLM-Driven Synthesis Planning for Quantum Dot Materials Development. 2748-2758 - Sayyed Jalil Mahdizadeh, Leif A. Eriksson:
iScore: A ML-Based Scoring Function for De Novo Drug Discovery. 2759-2772 - Clemens P. Spielvogel, Natalie Schindler, Christian Schröder, Sarah Luise Stellnberger, Wolfgang Wadsak, Markus Mitterhauser, Laszlo Papp, Marcus Hacker, Verena Pichler, Chrysoula Vraka:
Enhancing Blood-Brain Barrier Penetration Prediction by Machine Learning-Based Integration of Novel and Existing, In Silico and Experimental Molecular Parameters from a Standardized Database. 2773-2784 - Yaxing Wang, Xiang Liu, Yipeng Zhang, Xiangjun Wang, Kelin Xia:
Join Persistent Homology (JPH)-Based Machine Learning for Metalloprotein-Ligand Binding Affinity Prediction. 2785-2793 - Florian B. Hinz, Matthew R. Masters, Julia T. Nguyen, Amr H. Mahmoud, Markus A. Lill:
Accelerated Hydration Site Localization and Thermodynamic Profiling. 2794-2805 - Zhenjiao Du, Weimin Fu, Xiaolong Guo, Doina Caragea, Yonghui Li:
FusionESP: Improved Enzyme-Substrate Pair Prediction by Fusing Protein and Chemical Knowledge. 2806-2817 - Omer Tayfuroglu, Irem N. Zengin, M. Serdar Koca, Abdulkadir Kocak:
DeepConf: Leveraging ANI-ML Potentials for Exploring Local Minima with Application to Bioactive Conformations. 2818-2833 - Rachael A. Tindal, David W. Jeffery, Richard A. Muhlack:
Fourier Spectral Deconvolution to Describe Behaviors of pH-Dependent Monomeric and Self-Associated Anthocyanin Species. 2834-2844 - Florent Chevillard, Sandrine Hell, Elisa Liberatore:
BB-SAR: An Application for Data-driven Analysis and Rational Design of Medicinal Chemistry Series. 2845-2853 - Wenxiang Song, Le Xiong, Xinmin Li, Yuyang Zhang, Binya Wang, Guixia Liu, Weihua Li, Youjun Yang, Yun Tang:
Fluor-Predictor: An Interpretable Tool for Multiproperty Prediction and Retrieval of Fluorescent Dyes. 2854-2867 - Wenxiang Song, Ren Peng, Hongbo Yu, Meiling Zhan, Guixia Liu, Weihua Li, Guobin Ren, Bin Zhu, Yun Tang:
Cocry-pred: A Dynamic Resource Propagation Method for Cocrystal Prediction. 2868-2881 - Tieu-Long Phan, Klaus Weinbauer, Marcos E. González Laffitte, Yingjie Pan, Daniel Merkle, Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Peter F. Stadler:
SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases. 2882-2896 - Jeffrey M. Lotthammer, Alex S. Holehouse:
Disentangling Folding from Energetic Traps in Simulations of Disordered Proteins. 2897-2910 - Artur Bille, Victor Buchstaber, Evgeny Spodarev:
Some Open Mathematical Problems on Fullerenes. 2911-2923 - Arkadiusz Leniak, Wojciech Pietrus, Aleksandra Swiderska, Rafal Kurczab:
From NMR to AI: Do We Need 1H NMR Experimental Spectra to Obtain High-Quality logD Prediction Models? 2924-2939 - Solomon Y. Effah, Mark A. Hix, Alice R. Walker:
Strategic Design of Fluorescent Perylene-Modified Nucleic Acid Monomers: Position-, Phosphorylation-, and Linker-Dependent Control of Electron Transfer. 2940-2949 - Andrés Halabi Diaz, Mario Duque-Noreña, Elizabeth Rincón, Eduardo Chamorro:
Predicting the Mutagenic Activity of Nitroaromatics Using Conceptual Density Functional Theory Descriptors and Explainable No-Code Machine Learning Approaches. 2950-2960 - Kun Xi, Jinchu Liu, Lizhe Zhu:
Locating Multiple Transition Pathways for Complex Biomolecules. 2961-2973 - Xinyao Zheng, Ge Song, Zhengxin Li, Bowen Duan, Bofan Zhu, Hai-Feng Chen:
Nonbonded Parameter Optimization Improving Simulation of Intrinsically Disordered Phosphoproteins. 2974-2984 - Jiaxing Tang, Zhengdong Xu, Feng Wang, Lulu Guan, Bote Qi, Yu Zou:
Caffeine Inhibits Tau Aggregation and Destabilizes the Fibril Associated with Chronic Traumatic Encephalopathy: A REST2 and Conventional MD Simulations Study. 2985-2998 - Xuyang Qin, Jingjing Ji, Somya Chakraborty, Shikha Nangia:
Extending the PARCH Scale: Assessing Hydropathy of Proteins across Multiple Water Models. 2999-3009 - Kaichen Wang, Sean Xian Yu Lee, Chaitanya K. Jaladanki, Wei Shen Ho, Justin Jang Hann Chu, Hao Fan, Christina Li Lin Chai:
Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening. 3010-3021 - Wenbo Yu, David J. Weber, Alexander D. MacKerell Jr.:
Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation. 3022-3034 - Huynh Anh Duy, Tarapong Srisongkram:
Bidirectional Long Short-Term Memory (BiLSTM) Neural Networks with Conjoint Fingerprints: Application in Predicting Skin-Sensitizing Agents in Natural Compounds. 3035-3047 - Wenhao Wu, Shudong Wang, Kuijie Zhang, Hengxiao Li, Sibo Qiao, Yuanyuan Zhang, Shanchen Pang:
scMDCL: A Deep Collaborative Contrastive Learning Framework for Matched Single-Cell Multiomics Data Clustering. 3048-3063 - Fangfang Jin, Na Cheng, Lihua Wang, Bin Ye, Junfeng Xia:
FDPSM: Feature-Driven Prediction Modeling of Pathogenic Synonymous Mutations. 3064-3076 - Chaolin Song, Shiwen He, Yurong Qian, Xinhui Li, Yue Hu, Jiaying Chen, Jingfu Wang, Lei Deng:
DeepMVD: A Novel Multiview Dynamic Feature Fusion Model for Accurate Protein Function Prediction. 3077-3089 - Yanglan Gan, Shengnan Li, Guangwei Xu, Cairong Yan, Guobing Zou:
Multidependency Graph Convolutional Networks and Contrastive Learning for Drug Repositioning. 3090-3103 - Yu Li, Lin-Xuan Hou, Hai-Cheng Yi, Zhu-Hong You, Shi-Hong Chen, Jia Zheng, Yang Yuan, Cheng-Gang Mi:
MOLGAECL: Molecular Graph Contrastive Learning via Graph Auto-Encoder Pretraining and Fine-Tuning Based on Drug-Drug Interaction Prediction. 3104-3116
Volume 65, Number 7, 2025
- Issue Publication Information.
- Issue Editorial Masthead.
- Asli Yüksek, Batuhan Yikinç, Irem Nayir, Defne Alnigenis, Vahap Gazi Fidan, Tayyip Topuz, E. Demet Akten:
Structural Descriptors for Subunit Interface Regions in Homodimers: Effect of Lipid Membrane and Secondary Structure Type. 3117-3126 - Philipp Kuboth, Jan A. Meissner, Wassja A. Kopp, Jan Meisner:
AUTOGRAPH: Chemical Reaction Networks in 3D. 3127-3136 - Christopher Brasnett, Siewert J. Marrink:
MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies. 3137-3141 - Julia Subbotina, Panagiotis D. Kolokathis, Andreas Tsoumanis, Nikolaos K. Sidiropoulos, Ian Rouse, Iseult Lynch, Vladimir Lobaskin, Antreas Afantitis:
UANanoDock: A Web-Based UnitedAtom Multiscale Nanodocking Tool for Predicting Protein Adsorption onto Nanoparticles. 3142-3153 - Jinzhe Zeng, Timothy J. Giese, Duo Zhang, Han Wang, Darrin M. York:
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials. 3154-3160 - Adrian Racki, Kamil Paduszynski:
Recent Advances in the Modeling of Ionic Liquids Using Artificial Neural Networks. 3161-3175 - Kentarou Fuku, Takefumi Yoshida:
Unsupervised Machine Learning-Based Image Recognition of Raw Infrared Spectra: Toward Chemist-like Chemical Structural Classification and Beyond Numerical Data. 3176-3185 - Jianxiu Cai, Jielu Yan, Chonwai Un, Yapeng Wang, François-Xavier Campbell-Valois, Shirley W. I. Siu:
BERT-AmPEP60: A BERT-Based Transfer Learning Approach to Predict the Minimum Inhibitory Concentrations of Antimicrobial Peptides for Escherichia coli and Staphylococcus aureus. 3186-3202 - Qi Huang, Yedi Li, Lei Zhu, Wenjie Yu:
Hierarchical Deep Potential with Structure Constraints for Efficient Coarse-Grained Modeling. 3203-3214 - Herim Han, Bilal Shaker, Jin Hee Lee, Sunghwan Choi, Sanghee Yoon, Maninder Singh, Shaherin Basith, Minghua Cui, Sunil Ahn, Junyoung An, Soosung Kang, Min Sun Yeom, Sun Choi:
Employing Automated Machine Learning (AutoML) Methods to Facilitate the In Silico ADMET Properties Prediction. 3215-3225 - Marltan Wilson, Thomas Coudrat, Andrew Warden:
SELFprot: Effective and Efficient Multitask Finetuning Methods for Protein Parameter Prediction. 3226-3238 - Jiaxin Yan, Haiyuan Wang, Wensheng Yang, Xiaonan Ma, Yajing Sun, Wenping Hu:
ChiGNN: Interpretable Algorithm Framework of Molecular Chiral Knowledge-Embedding and Stereosensitive Property Prediction. 3239-3247 - Dominga Evangelista, Elliot Nelson, Rachael Skyner, Ben Tehan, Mattia Bernetti, Marinella Roberti, Maria Laura Bolognesi, Giovanni Bottegoni:
Application of Deep Learning to Predict the Persistence, Bioaccumulation, and Toxicity of Pharmaceuticals. 3248-3261 - Jian Wang, Nikolay V. Dokholyan:
Leveraging Transfer Learning for Predicting Protein-Small-Molecule Interaction Predictions. 3262-3269 - Rubens C. Souza, Julio C. Duarte, Ronaldo R. Goldschmidt, Itamar Borges Jr.:
Predicting Fluorescence Emission Wavelengths and Quantum Yields via Machine Learning. 3270-3281 - Zhen Chang, Li Feng, Hong-Tao Xue, Yan-Hong Yang, Jun-Qiang Ren, Fu-Ling Tang, Xue-Feng Lu, Jun-Chen Li:
Deep-Learning Potential Molecular Dynamics Study on Nanopolycrystalline Al-Er Alloys: Effects of Er Concentration, Grain Boundary Segregation, and Grain Size on Plastic Deformation. 3282-3293 - Xiaomeng Liu, Qin Li, Xiao Yan, Lingling Wang, Jiayue Qiu, Xiaojun Yao, Huanxiang Liu:
A Specialized and Enhanced Deep Generation Model for Active Molecular Design Targeting Kinases Guided by Affinity Prediction Models and Reinforcement Learning. 3294-3308 - Junyu Zhou, Chen Li, Yu Yue, Yong Kwan Kim, Sunmin Park:
Multitarget Natural Compounds for Ischemic Stroke Treatment: Integration of Deep Learning Prediction and Experimental Validation. 3309-3323 - Zhihao Guan, Xiu Jin, Xiaodan Zhang:
MFF-nDA: A Computational Model for ncRNA-Disease Association Prediction Based on Multimodule Fusion. 3324-3342 - Sargol Mazraedoost, Hadi Sedigh Malekroodi, Petar Zuvela, Myunggi Yi, J. Jay Liu:
Prediction of Chromatographic Retention Time of a Small Molecule from SMILES Representation Using a Hybrid Transformer-LSTM Model. 3343-3356 - Qiufen Chen, Yuewei Zhang, Jiali Gao, Jun Zhang:
CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides. 3357-3369 - Yi-Qi Chen, Tao Yu, Zheng-Qi Song, Chen-Yu Wang, Jiang-Tao Luo, Yong Xiao, Heng Qiu, Qing-Qing Wang, Hai-Ming Jin:
Application of Large Language Models in Drug-Induced Osteotoxicity Prediction. 3370-3379 - Jiashun Fu, Xuyang Liu, Ruijie Deng, Xiue Jiang, Wensheng Cai, Haohao Fu, Xueguang Shao:
Accurate Prediction of CRISPR/Cas13a Guide Activity Using Feature Selection and Deep Learning. 3380-3387 - Yu Hamakawa, Tomoyuki Miyao:
Understanding Conformation Importance in Data-Driven Property Prediction Models. 3388-3404 - Fabian Grünewald, Leif Seute, Riccardo Alessandri, Mélanie König, Peter C. Kroon:
CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions. 3405-3419 - Zhiting Zhang, Jia Qiu, Jiajun Zheng, Zhunzhun Yu, Lebin Su, Qianghua Lin, Chonghuan Zhang, Kuangbiao Liao:
Enhanced Regioselectivity Prediction of sp2 C-H Halogenation via Negative Data Augmentation and Multimodel Integration. 3420-3430 - Erik Lindahl, Ran Friedman:
Estimation of Absolute Binding Free Energies for Drugs That Bind Multiple Proteins. 3431-3438 - Martina Rajic, Jernej Stare:
Investigation of Electrostatic Effects on Enyzme Catalysis: Insights from Computational Simulations of Monoamine Oxidase A Pathological Variants Leading to the Brunner Syndrome. 3439-3450 - Yeongsu Cho, Jakob Teetz, Heather J. Kulik:
Assessing UFF and DFT-Tuned Force Fields for Predicting Experimental Isotherms of MOFs. 3451-3460 - Jongyoon Bae, Bjarne Kreitz, Andrew A. Peterson, C. Franklin Goldsmith:
Influence of Coverage Dependence on the Thermophysical Properties of Adsorbates and Its Impact on Microkinetic Models. 3461-3476 - Martín Otero-Lema, Raúl Lois-Cuns, Miguel A. Boado, Hadrián Montes-Campos, Trinidad Méndez-Morales, Luis M. Varela:
KUTE: Green-Kubo Uncertainty-Based Transport Coefficient Estimator. 3477-3487 - Jorge Alberto Sanchez Alvarez, Luis López-Sosa, Andreas M. Köster, Patrizia Calaminici:
Constrained Structure Minimizations on Hyperspheres for Minimum Energy Path Following. 3488-3501 - Audrey V. Conner, Lauren M. Kim, Patrick A. Fagan, Drew P. Harding, Steven E. Wheeler:
Stacking Interactions of Druglike Heterocycles with Nucleobases. 3502-3516 - Lin Feng, Xiangzheng Fu, Zhenya Du, Yuting Guo, Linlin Zhuo, Yan Yang, Dong-Sheng Cao, Xiaojun Yao:
MultiCTox: Empowering Accurate Cardiotoxicity Prediction through Adaptive Multimodal Learning. 3517-3528 - Sijie Liu, Jie Wu, Ya Chen, Clemens Alexander Wolf, Matthias Bureik, Johannes Kirchmair, Mario Andrea Marchisio, Gerhard Wolber:
Integrated Virtual Screening Approach Identifies New CYP19A1 Inhibitors. 3529-3543 - Christina Bergonzo, Alexander Grishaev:
Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game. 3544-3554 - Orathai Kaewkham, Duangkamol Gleeson, Poowadon Fukasem, Jirapat Santatiwongchai, Donald J. L. Jones, Robert G. Britton, Matthew Paul Gleeson:
Probing the Effect of Protein and Inhibitor Conformational Flexibility on the Reaction of Rocelitinib-Like Covalent Inhibitors of Epidermal Growth Factor Receptor. A Quantum Mechanics/Molecular Mechanics Study. 3555-3567 - Tomás F. D. Silva, Giovanni Bussi:
Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations. 3568-3580 - Tobias M. Prass, Kresten Lindorff-Larsen, Patrick Garidel, Michaela Blech, Lars V. Schäfer:
Optimized Protein-Excipient Interactions in the Martini 3 Force Field. 3581-3592 - Mac Kevin E. Braza, Özlem Demir, Surl-Hee Ahn, Clare Morris, Carla Calvó-Tusell, Kelly L. McGuire, Bárbara de la Peña Avalos, Michael A. Carpenter, Yanjun Chen, Lorenzo Casalino, Hideki Aihara, Mark A. Herzik, Reuben S. Harris, Rommie E. Amaro:
Regulatory Interactions between APOBEC3B N- and C-Terminal Domains. 3593-3604 - Karim Malekzadeh, Gül H. Zerze:
Optimizing On-the-Fly Probability Enhanced Sampling for Complex RNA Systems: Sampling Free Energy Surfaces of an H-Type Pseudoknot. 3605-3614 - Marco A. Ramírez-Martínez, Nina Pastor:
Role of Cre Dynamics in Autoinhibition and Priming. 3615-3627 - Shreya Bhattacharya, Priyadarshi Satpati:
Energetics of Expanded PAM Readability by Engineered Cas9-NG. 3628-3639 - Fabio Mazza, Davide Dalfovo, Alessio Bartocci, Gianluca Lattanzi, Alessandro Romanel:
Integrative Computational Analysis of Common EXO5 Haplotypes: Impact on Protein Dynamics, Genome Stability, and Cancer Progression. 3640-3654 - Jian Jiang, Long Chen, Yueying Zhu, Yazhou Shi, Huahai Qiu, Bengong Zhang, Tianshou Zhou, Guo-Wei Wei:
Proteomic Learning of Gamma-Aminobutyric Acid (GABA) Receptor-Mediated Anesthesia. 3655-3668 - Xiaoyue Ji, Junjie Zhu, Bozitao Zhong, Zhengxin Li, Taeyoung Choi, Xiaochen Cui, Ting Wei, Hai-Feng Chen:
Personalized Energy Adaptation through Reweighting Learning (PEARL) Force Field for Intrinsically Disordered Proteins. 3669-3681 - Minghao Liu, Kaiyu Wang, Yan Zhang, Xue Zhou, Wannan Li, Weiwei Han:
Mechanistic Study of Protein Interaction with Natto Inhibitory Peptides Targeting Xanthine Oxidase: Insights from Machine Learning and Molecular Dynamics Simulations. 3682-3696 - Balaji Selvam, Arnav Paul, Ya-Chi Yu, Li-Qing Chen, Diwakar Shukla:
SWEET Family Transporters Act as Water-Conducting Carrier Proteins in Plants. 3697-3705 - Emilio Gallicchio:
Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer Method with Coordinate Swapping. 3706-3714 - Ashraf Mohamed, Bernard R. Brooks, Muhamed Amin:
Leveraging-Induced Polarization for Drug Discovery: Efficient IC50 Prediction Using Minimal Features. 3715-3722 - Bogdan Zorila, George Necula, Lorant Janosi, Ioan Turcu, Mihaela Bacalum, Mihai Radu:
Interaction of Arginine and Tryptophan-Rich Short Antimicrobial Peptides with Membrane Models: A Combined Fluorescence, Simulations, and Theoretical Approach. 3723-3736 - Eric A. Chen, Yingkai Zhang:
Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds? 3737-3748 - Hengliang Guo, Congxiang Zhang, Jiandong Shang, Dujuan Zhang, Yang Guo, Kang Gao, Kecheng Yang, Xu Gao, Dezhong Yao, Wanting Chen, Mengfan Yan, Gang Wu:
Drug-Target Affinity Prediction Based on Topological Enhanced Graph Neural Networks. 3749-3760 - Liang Zhang, Kuan Luo, Ziyi Zhou, Yuanxi Yu, Fan Jiang, Banghao Wu, Mingchen Li, Liang Hong:
A Deep Retrieval-Enhanced Meta-Learning Framework for Enzyme Optimum pH Prediction. 3761-3770 - Chengsong Wu, Yuanyuan Ren, Yang Li, Yue Cui, Liyao Zhang, Pan Zhang, Xuejiao Zhang, Shangguang Kan, Chan Zhang, Yuyan Xiong:
Identification and Experimental Validation of NETosis-Mediated Abdominal Aortic Aneurysm Gene Signature Using Multi-omics, Machine Learning, and Mendelian Randomization. 3771-3788 - Shuwen Xiong, Jiajie Cai, Hua Shi, Feifei Cui, Zilong Zhang, Leyi Wei:
UMPPI: Unveiling Multilevel Protein-Peptide Interaction Prediction via Language Models. 3789-3799 - Yaxian Cai, Ziying Zhang, Xiangyu Xu, Liang Xu, Yu Chen, Guijun Zhang, Xiaogen Zhou:
Fitting Atomic Structures into Cryo-EM Maps by Coupling Deep Learning-Enhanced Map Processing with Global-Local Optimization. 3800-3811 - Lingrong Zhang, Taigang Liu:
ATP-Pred: Prediction of Protein-ATP Binding Residues via Fusion of Residue-Level Embeddings and Kolmogorov-Arnold Network. 3812-3826 - Yinchun Su, Jiashuo Wu, Xilong Zhao, Yue Hao, Ziyi Wang, Yongbao Zhang, Yujie Tang, Bingyue Pan, Guangyou Wang, Qingfei Kong, Junwei Han:
Knowledge-Based Artificial Intelligence System for Drug Prioritization. 3827-3840 - Jingfu Wang, Jiaying Chen, Yue Hu, Chaolin Song, Xinhui Li, Yurong Qian, Lei Deng:
DeepMFFGO: A Protein Function Prediction Method for Large-Scale Multifeature Fusion. 3841-3853 - Chunting Liu, Sudong Cai, Tong Pan, Hiroyuki Ogata, Jiangning Song, Tatsuya Akutsu:
SFM-Net: Selective Fusion of Multiway Protein Feature Network for Predicting Binding Affinity Changes upon Mutations. 3854-3865 - Chengyuan Yue, Baiyu Chen, Fei Pan, Ze Wang, Hongbo Yu, Guixia Liu, Weihua Li, Rui Wang, Yun Tang:
TCnet: A Novel Strategy to Predict Target Combination of Alzheimer's Disease via Network-Based Methods. 3866-3878
Volume 65, Number 8, 2025
- Issue Editorial Masthead.
- Issue Publication Information.
- Emily H. Chaisson, Frederick A. Heberle, Milka Doktorova:
Quantifying Acyl Chain Interdigitation in Simulated Bilayers via Direct Transbilayer Interactions. 3879-3885 - Philipp Döpner, Stefan Kemnitz, Mark Doerr, Lukas Schulig:
af3cli: Streamlining AlphaFold3 Input Preparation. 3886-3891 - Yuchen Wang, D. Sulalith N. D. Samarasinghe, Hao Deng, Bin Liu, Christine M. Aikens:
Gaussian Process Approach to Constructing Transferable Force Fields for Thiolate-Protected Gold Nanoclusters. 3892-3902 - Yu Shee, Anton Morgunov, Haote Li, Victor S. Batista:
DirectMultiStep: Direct Route Generation for Multistep Retrosynthesis. 3903-3914 - Ziyu Wei, Zhengyu Wang, Chang Tang:
Dynamic Prediction of Drug-Target Interactions via Cross-Modal Feature Mapping with Learnable Association Information. 3915-3927 - Wuling Zhao, Minxia Zhou, Jialin Shao, Jingzheng Ren, Yusha Hu, Yulin Han, Yi Man:
Crystal Structure Prediction Using a Self-Attention Neural Network and Semantic Segmentation. 3928-3943 - Muzammil Kabier, Nicola Gambacorta, Fulvio Ciriaco, Fabrizio Mastrolorito, Sunil Kumar, Bijo Mathew, Orazio Nicolotti:
PoseidonQ: A Free Machine Learning Platform for the Development, Analysis, and Validation of Efficient and Portable QSAR Models for Drug Discovery. 3944-3954 - Yi He, Zhenglin Tian, Jingxian Zheng, Haohao Wang, Lu Han, Weiwei Han:
Prediction of Umami Peptides Based on a Large Language Model of Proteins. 3955-3962 - Rishabh D. Guha, Santiago Vargas, Evan Walter Clark Spotte-Smith, Alexander Rizzolo Epstein, Maxwell C. Venetos, Ryan Kingsbury, Mingjian Wen, Samuel M. Blau, Kristin A. Persson:
HEPOM: Using Graph Neural Networks for the Accelerated Predictions of Hydrolysis Free Energies in Different pH Conditions. 3963-3975 - Ayush Garg, Narayanan Ramamurthi, Shyam Sundar Das:
Addressing Imbalanced Classification Problems in Drug Discovery and Development Using Random Forest, Support Vector Machine, AutoGluon-Tabular, and H2O AutoML. 3976-3989 - Thomas Kelly, Song Xia, Jieyu Lu, Yingkai Zhang:
Unified Deep Learning of Molecular and Protein Language Representations with T5ProtChem. 3990-3998 - Maximilian Fleck, Samir Darouich, Jürgen Pleiss, Niels Hansen, Marcelle B. M. Spera:
Physics-Informed Multifidelity Gaussian Process: Modeling the Effect of Water and Temperature on the Viscosity of a Deep Eutectic Solvent. 3999-4009 - Ali Esmaeili, Hesamedin Hekmatmehr, Mohammad Moheisen, Saeid Atashrouz, Ali Abedi, Ahmad Mohaddespour:
Heat Capacity of Ionic Liquids: Toward Interpretable Chemical Structure-Based Machine Learning Approaches. 4010-4026 - The-Chuong Trinh, Pierre Falson, Viet-Khoa Tran-Nguyen, Ahcène Boumendjel:
Ligand-Based Drug Discovery Leveraging State-of-the-Art Machine Learning Methodologies Exemplified by Cdr1 Inhibitor Prediction. 4027-4042 - Dmitriy M. Makarov, Nikolai N. Kalikin, Yury A. Budkov, Pavel Gurikov, Sergey E. Kruchinin, Abolghasem Jouyban, Michael G. Kiselev:
Improved Solubility Predictions in scCO2 Using Thermodynamics-Informed Machine Learning Models. 4043-4056 - Andrii V. Kyrsanov, Ihor V. Tkachenko, Nataliya A. Shtil, Konstantin S. Gavrilenko, Olexandr Ye. Pashenko, Duncan B. Judd, Sergey V. Ryabukhin, Dmitriy M. Volochnyuk:
Chemistry Meets Biology: Cross-Disciplinary Evaluation of Drug Discovery Databases. 4057-4066 - Michael Faran, Gili Bisker:
Nonequilibrium Self-Assembly Control by the Stochastic Landscape Method. 4067-4080 - Francesc Sabanés Zariquiey, Stephen E. Farr, Stefan Doerr, Gianni De Fabritiis:
QuantumBind-RBFE: Accurate Relative Binding Free Energy Calculations Using Neural Network Potentials. 4081-4089 - Maocai Yan, Xinfa Ding, Likun Zhao, Xudong Lü, Hai-Yan He, Shuai Fan, Zhaoyong Yang:
Mechanistic Insights into the Nonenzymatic Biosynthesis of Artemisinin and Related Natural Products: A Quantum Chemical Study. 4090-4106 - José Fiorote, João Alves, Letícia Stock, Werner Treptow:
Investigating Statistical Conditions of Coevolutionary Signals that Enable Algorithmic Predictions of Protein Partners. 4107-4115 - Daichi Hayakawa, Hiroaki Gouda:
Three-Dimensional CH/π and CH/N Interactions from Quantum-Mechanical and Database Analyses. 4116-4127 - Ana Díaz-Fernández, Carmen S. Ciudad, Natalia Díaz, Dimas Suárez, Noemí de-los-Santos-Álvarez, María Jesús Lobo-Castañón:
Refinement and Truncation of DNA Aptamers Based on Molecular Dynamics Simulations: Computational Protocol and Experimental Validation. 4128-4136 - Natthiti Chiangraeng, Norio Yoshida, Haruyuki Nakano, Apinpus Rujiwatra, Piyarat Nimmanpipug:
Influence of Water/Ethanol Mixing Ratio on Gemcitabine Binding to Cucurbit-7-uril Based on Molecular Dynamics Simulations and Three-Dimensional Reference Interaction Site Model. 4137-4147 - Azam Rashidian, Sini Pitkänen, Vinicius Gonçalves Maltarollo, Ulrich Schoppmeier, Ekaterina Shevchenko, Prasanthi Medarametla, Antti Poso, Jenni Küblbeck, Paavo Honkakoski, Thales Kronenberger:
Look What You Made Me Do: Discerning Feature for Classification of Endocrine-Disrupting Chemical Binding to Steroid Hormone Receptors. 4148-4162 - Sunandini Swain, Atanu K. Metya:
Exploring Metformin's Therapeutic Potential for Alzheimer's Disease: An In-Silico Perspective Using Well-Tempered Funnel Metadynamics. 4163-4172 - Miao Yang, Jingran Wang, Ziyun Zhou, Wentian Li, Gennady Verkhivker, Fei Xiao, Guang Hu:
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder. 4173-4188 - Jianzhong Chen, Jian Wang, Wanchun Yang, Lu Zhao, Jing Su:
Activity Regulation and Conformation Response of Janus Kinase 3 Mediated by Phosphorylation: Exploration from Correlation Network Analysis and Markov Model. 4189-4205 - Changsheng Zhang, Fanhao Wang, Tiantian Zhang, Yang Yang, Liying Wang, Xiaoling Zhang, Luhua Lai:
De Novo Design of Cyclic Peptide Binders Based on Fragment Docking and Assembling. 4206-4218 - Shan Sun, David J. Huggins:
Comparing Molecules Generated by MMPDB and REINVENT4 with Ideas from Drug Discovery Design Teams. 4219-4231 - Joshua Zhi En Tan, Junjie Wee, Xue Gong, Kelin Xia:
Topology-Enhanced Machine Learning Model (Top-ML) for Anticancer Peptide Prediction. 4232-4242
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