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The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions JOURNAL ARTICLE published 24 August 2020 in Journal of Chemical Information and Modeling Research funded by Terry Fox Research Institute (1062) |
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MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design JOURNAL ARTICLE published 8 August 2022 in Journal of Chemical Information and Modeling Research funded by Sandia National Laboratories (DE-NA-0003525) | Lawrence Berkeley National Laboratory (DE-AC02-05CH11231) |
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Serendipitous Discovery of Short Peptides from Natural Products as Tyrosinase Inhibitors JOURNAL ARTICLE published 24 November 2014 in Journal of Chemical Information and Modeling Research funded by National Science Council Taiwan (100-2320-B-077-004-MY2,103-2320-B-077-001-MY3) | National Research Institute of Chinese Medicine, Taiwan (103T51-11) |
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Model-Free Drug-Likeness from Fragments JOURNAL ARTICLE published 23 August 2010 in Journal of Chemical Information and Modeling |
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Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods JOURNAL ARTICLE published 26 March 2018 in Journal of Chemical Information and Modeling |
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Combining Group-Contribution Concept and Graph Neural Networks Toward Interpretable Molecular Property Models JOURNAL ARTICLE published 13 February 2023 in Journal of Chemical Information and Modeling |
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Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting JOURNAL ARTICLE published 25 September 2023 in Journal of Chemical Information and Modeling Research funded by Division of Graduate Education (2020298734) | Office of Science (DE-AC05-00OR22725) | National Science Foundation (1835449,1931512,ACI-1548562,MCB-1942763) |
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Highly SpecIfic and Sensitive Pharmacophore Model for Identifying CXCR4 Antagonists. Comparison with Docking and Shape-Matching Virtual Screening Performance JOURNAL ARTICLE published 24 May 2013 in Journal of Chemical Information and Modeling |
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Mebendazole’s Conformational Space and Its Predicted Binding to Human Heat-Shock Protein 90 JOURNAL ARTICLE published 8 August 2022 in Journal of Chemical Information and Modeling |
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A Contribution to the Drug Resistance Mechanism of Darunavir, Amprenavir, Indinavir, and Saquinavir Complexes with HIV-1 Protease Due to Flap Mutation I50V: A Systematic MM–PBSA and Thermodynamic Integration Study JOURNAL ARTICLE published 26 August 2013 in Journal of Chemical Information and Modeling |
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Binding Analysis of Some Classical Acetylcholinesterase Inhibitors: Insights for a Rational Design Using Free Energy Perturbation Method Calculations with QM/MM MD Simulations JOURNAL ARTICLE published 24 April 2017 in Journal of Chemical Information and Modeling Research funded by Generalitat Valenciana (2011/040,ACOMP/2014/270,ACOMP/2015/1202,PrometeoII/2014/022) | Ministerstwo Nauki i Szkolnictwa Wyzszego (0478/IP3/2015/73) | Universitat Jaume I (P1?1B2013-40,P1?1B2013-58) | Ministerio de Econom?a y Competitividad (CTQ2015-65207-P) | Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (306945/2015-0) |
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Structural Protein–Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study JOURNAL ARTICLE published 22 September 2014 in Journal of Chemical Information and Modeling |
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De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder JOURNAL ARTICLE published 10 July 2023 in Journal of Chemical Information and Modeling Research funded by Thailand Science Research and Innovation (FRB650048/0164) |
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Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches JOURNAL ARTICLE published 24 October 2016 in Journal of Chemical Information and Modeling |
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Calcium Ion Binding to the Mutants of Calmodulin: A Structure-Based Computational Predictive Model of Binding Affinity Using a Charge Scaling Approach in Molecular Dynamics Simulation JOURNAL ARTICLE published 13 June 2022 in Journal of Chemical Information and Modeling Research funded by Department of Biotechnology , Ministry of Science and Technology (BT/PR/40251/BITS/137/11/2021,BT/PR27604/BID/7/826/2018) |
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Doping Effects on the Performance of Paired Metal Catalysts for the Hydrogen Evolution Reaction JOURNAL ARTICLE published 28 May 2019 in Journal of Chemical Information and Modeling |
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Direct Observation of Seeded Conformational Conversion of hIAPP In Silico Reveals the Mechanisms for Morphological Dependence and Asymmetry of Fibril Growth JOURNAL ARTICLE published 25 September 2023 in Journal of Chemical Information and Modeling Research funded by National Natural Science Foundation of China (11904189,T2250710182) | U.S. Department of Health and Human Services (R35GM145409) | Ningbo Top Medical and Health Research Program (2022020304) |
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Classification Model for the Second Extracellular Loop of Class A GPCRs JOURNAL ARTICLE published 14 February 2022 in Journal of Chemical Information and Modeling |
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Binding Affinity Prediction for Protein–Ligand Complexes Based on β Contacts and B Factor JOURNAL ARTICLE published 25 November 2013 in Journal of Chemical Information and Modeling |
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Capturing the Recognition Dynamics of para-Sulfonato-calix[4]arenes by Cytochrome c: Toward a Quantitative Free Energy Assessment JOURNAL ARTICLE published 26 December 2022 in Journal of Chemical Information and Modeling |