Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use. - Gary Tresadern; Dimitris K. Agrafiotis (J. Chem. Inf. Model., 2009)

Recognizing Pitfalls in Virtual Screening: A Critical Review. - Thomas Scior; Andreas Bender 002; Gary Tresadern; José L. Medina-Franco; Karina Martínez-Mayorga; Thierry Langer; Karina Cuanalo-Contreras; Dimitris K. Agrafiotis (J. Chem. Inf. Model., 2012)

Application of Free Energy Perturbation for the Design of BACE1 Inhibitors. - Myriam Ciordia; Laura Pérez-Benito; Francisca Delgado; Andrés A. Trabanco; Gary Tresadern (J. Chem. Inf. Model., 2016)

Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling. - Gary Tresadern; Andrés A. Trabanco; Laura Pérez-Benito; John P. Overington; Herman W. T. van Vlijmen; Gerard J. P. van Westen (J. Chem. Inf. Model., 2017)

The size matters? A computational tool to design bivalent ligands. - Laura Pérez-Benito; Andrew Henry; Minos-Timotheos Matsoukas; Laura Lopez; Daniel Pulido; Miriam Royo; Arnau Cordomí; Gary Tresadern; Leonardo Pardo (Bioinform., 2018)

Mechanisms Underlying Allosteric Molecular Switches of Metabotropic Glutamate Receptor 5. - Claudia Llinas del Torrent; Nil Casajuana-Martin; Leonardo Pardo; Gary Tresadern; Laura Pérez-Benito (J. Chem. Inf. Model., 2019)

Limitations of Ligand-Only Approaches for Predicting the Reactivity of Covalent Inhibitors. - Angus Voice; Gary Tresadern; Herman van Vlijmen; Adrian J. Mulholland (J. Chem. Inf. Model., 2019)

Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation. - Francesca Deflorian; Laura Pérez-Benito; Eelke B. Lenselink; Miles Congreve; Herman W. T. van Vlijmen; Jonathan S. Mason; Chris de Graaf; Gary Tresadern (J. Chem. Inf. Model., 2020)

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. - Yuriy Khalak; Gary Tresadern; Bert L. de Groot; Vytautas Gapsys (J. Comput. Aided Mol. Des., 2021)

Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. - Lorenzo D'amore; David F. Hahn; David L. Dotson; Joshua T. Horton; Jamshed Anwar; Ian Craig; Thomas Fox; Alberto Gobbi; Sirish Kaushik Lakkaraju; Xavier Lucas; Katharina Meier; David L. Mobley; et al. (J. Chem. Inf. Model., 2022)

Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. - Vytautas Gapsys; David F. Hahn; Gary Tresadern; David L. Mobley; Markus Rampp; Bert L. de Groot (J. Chem. Inf. Model., 2022)

The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions. - Gary Tresadern; Kanaka Tatikola; Javier Cabrera; Lingle Wang; Robert Abel; Herman van Vlijmen; Helena Geys (J. Chem. Inf. Model., 2022)

Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery. - Francesc Sabanés Zariquiey; Edgar Jacoby; Ann Vos; Herman W. T. van Vlijmen; Gary Tresadern; Jeremy N. Harvey (J. Chem. Inf. Model., 2022)

To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough. - Mary Pitman; David F. Hahn; Gary Tresadern; David L. Mobley (J. Chem. Inf. Model., 2023)

MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands. - Sridip Parui; James C. Robertson; Sandeep Somani; Gary Tresadern; Cong Liu 031; Ken A. Dill (J. Chem. Inf. Model., 2023)

ACEGEN: Reinforcement Learning of Generative Chemical Agents for Drug Discovery. - Albert Bou; Morgan Thomas; Sebastian Dittert; Carles Navarro; Maciej Majewski; Ye Wang 024; Shivam Patel; Gary Tresadern; Mazen Ahmad; Vincent Moens; Woody Sherman; Simone Sciabola; et al. (J. Chem. Inf. Model., 2024)

Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. - David F. Hahn; Vytautas Gapsys; Bert L. de Groot; David L. Mobley; Gary Tresadern (J. Chem. Inf. Model., 2024)

PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models. - Morgan Thomas; Mazen Ahmad; Gary Tresadern; Gianni De Fabritiis (J. Cheminformatics, 2024)

Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy. - Sudarshan Behera; David F. Hahn; Carter J. Wilson; Simone Marsili; Gary Tresadern; Vytautas Gapsys; Bert L. de Groot (J. Chem. Inf. Model., 2025)