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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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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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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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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 |
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Inhibition of β-Amyloid Channels with a Drug Candidate wgx-50 Revealed by Molecular Dynamics Simulations JOURNAL ARTICLE published 27 November 2017 in Journal of Chemical Information and Modeling Research funded by Ministry of Science and Technology of the People's Republic of China (2016YFA0501703) |
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New Features of the Open Source Monte Carlo Software Brick-CFCMC: Thermodynamic Integration and Hybrid Trial Moves JOURNAL ARTICLE published 23 August 2021 in Journal of Chemical Information and Modeling Research funded by Total (n.a.) | Nederlandse Organisatie voor Wetenschappelijk Onderzoek (n.a.) |
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Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography JOURNAL ARTICLE published 8 May 2023 in Journal of Chemical Information and Modeling |
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Are the Absorption Spectra of Doxorubicin Properly Described by Considering Different Tautomers? JOURNAL ARTICLE published 24 February 2020 in Journal of Chemical Information and Modeling Research funded by Funda??o de Amparo ? Ci?ncia e Tecnologia do Estado de Pernambuco (APQ - 0675-1.06/14) | Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (308338/2018-9,421733/2018-7) | Funda??o de Apoio ? Pesquisa e ? Inova??o Tecnol?gica do Estado de Sergipe (019.203.01074/2011-1) |
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Issue Publication Information JOURNAL ARTICLE published 27 February 2023 in Journal of Chemical Information and Modeling |
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Issue Publication Information JOURNAL ARTICLE published 9 January 2023 in Journal of Chemical Information and Modeling |
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Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening JOURNAL ARTICLE published 24 June 2019 in Journal of Chemical Information and Modeling Research funded by Research Councils UK (EP/L016044/1) | Seventh Framework Programme (Marie Curie Initial Training Network STARS PITN-GA-2009-238490) |