Gary Tresadern

24 papers Journal 24
YearRankTypeTitle / Venue / Authors
2025 J jnl
C2PO: an ML-powered optimizer of the membrane permeability of cyclic peptides through chemical modification.
J. Cheminformatics
Roy Aerts, Joris Tavernier, Alan Kerstjens, Mazen Ahmad, José Carlos Gómez-Tamayo, Gary Tresadern, Hans De Winter
2025 J jnl
MolAgent: Biomolecular Property Estimation in the Agentic Era.
J. Chem. Inf. Model.
José Carlos Gómez-Tamayo, Joris Tavernier, Roy Aerts, Natalia Dyubankova, Dries Van Rompaey, Sairam Menon, Marvin N. Steijaert, Jörg Kurt Wegner, Hugo Ceulemans, Gary Tresadern, Hans De Winter, Mazen Ahmad
2025 J jnl
Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy.
J. Chem. Inf. Model.
Sudarshan Behera, David F. Hahn, Carter J. Wilson, Simone Marsili, Gary Tresadern, Vytautas Gapsys, Bert L. de Groot
2025 J jnl
REINFORCE-ING Chemical Language Models for Drug Discovery.
J. Chem. Inf. Model.
Morgan C. Thomas, Albert Bou, José Carlos Gómez-Tamayo, Gary Tresadern, Mazen Ahmad, Gianni De Fabritiis
2025 J jnl
Spatio-temporal learning from molecular dynamics simulations for protein-ligand binding affinity prediction.
Bioinform.
Pierre-Yves Libouban, Camille Parisel, Maxime Song, Samia Aci-Sèche, José Carlos Gómez-Tamayo, Gary Tresadern, Pascal Bonnet
2024 J jnl
ACEGEN: Reinforcement Learning of Generative Chemical Agents for Drug Discovery.
J. Chem. Inf. Model.
Albert Bou, Morgan C. Thomas, Sebastian Dittert, Carles Navarro, Maciej Majewski, Ye Wang, Shivam Patel, Gary Tresadern, Mazen Ahmad, Vincent Moens, Woody Sherman, Simone Sciabola, Gianni De Fabritiis
2024 J jnl
ACEGEN: Reinforcement learning of generative chemical agents for drug discovery.
CoRR
Albert Bou, Morgan C. Thomas, Sebastian Dittert, Carles Navarro Ramírez, Maciej Majewski, Ye Wang, Shivam Patel, Gary Tresadern, Mazen Ahmad, Vincent Moens, Woody Sherman, Simone Sciabola, Gianni De Fabritiis
2024 J jnl
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions.
J. Chem. Inf. Model.
David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary Tresadern
2024 J jnl
PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models.
J. Cheminformatics
Morgan C. Thomas, Mazen Ahmad, Gary Tresadern, Gianni De Fabritiis
2023 J jnl
MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands.
J. Chem. Inf. Model.
Sridip Parui, James C. Robertson, Sandeep Somani, Gary Tresadern, Cong Liu, Ken A. Dill
2023 J jnl
To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough.
J. Chem. Inf. Model.
Mary Pitman, David F. Hahn, Gary Tresadern, David L. Mobley
2022 J jnl
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field.
J. Chem. Inf. Model.
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, Arjun Narayanan, Christina E. M. Schindler, William C. Swope, Pieter J. in 't Veld, Jeffrey Wagner, Bai Xue, Gary Tresadern
2022 J jnl
Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery.
J. Chem. Inf. Model.
Francesc Sabanés Zariquiey, Edgar Jacoby, Ann Vos, Herman W. T. van Vlijmen, Gary Tresadern, Jeremy N. Harvey
2022 J jnl
Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design.
J. Chem. Inf. Model.
Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, Bert L. de Groot
2022 J jnl
The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions.
J. Chem. Inf. Model.
Gary Tresadern, Kanaka Tatikola, Javier Cabrera, Lingle Wang, Robert Abel, Herman van Vlijmen, Helena Geys
2021 J jnl
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software.
J. Comput. Aided Mol. Des.
Yuriy Khalak, Gary Tresadern, Bert L. de Groot, Vytautas Gapsys
2020 J jnl
Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation.
J. Chem. Inf. Model.
Francesca Deflorian, Laura Pérez-Benito, Eelke B. Lenselink, Miles Congreve, Herman W. T. van Vlijmen, Jonathan S. Mason, Chris de Graaf, Gary Tresadern
2019 J jnl
Limitations of Ligand-Only Approaches for Predicting the Reactivity of Covalent Inhibitors.
J. Chem. Inf. Model.
Angus Voice, Gary Tresadern, Herman van Vlijmen, Adrian J. Mulholland
2019 J jnl
Mechanisms Underlying Allosteric Molecular Switches of Metabotropic Glutamate Receptor 5.
J. Chem. Inf. Model.
Claudia Llinas del Torrent, Nil Casajuana-Martin, Leonardo Pardo, Gary Tresadern, Laura Pérez-Benito
2018 J jnl
The size matters? A computational tool to design bivalent ligands.
Bioinform.
Laura Pérez-Benito, Andrew Henry, Minos-Timotheos Matsoukas, Laura Lopez, Daniel Pulido, Miriam Royo, Arnau Cordomí, Gary Tresadern, Leonardo Pardo
2017 J jnl
Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling.
J. Chem. Inf. Model.
Gary Tresadern, Andrés A. Trabanco, Laura Pérez-Benito, John P. Overington, Herman W. T. van Vlijmen, Gerard J. P. van Westen
2016 J jnl
Application of Free Energy Perturbation for the Design of BACE1 Inhibitors.
J. Chem. Inf. Model.
Myriam Ciordia, Laura Pérez-Benito, Francisca Delgado, Andrés A. Trabanco, Gary Tresadern
2012 J jnl
Recognizing Pitfalls in Virtual Screening: A Critical Review.
J. Chem. Inf. Model.
Thomas Scior, Andreas Bender, Gary Tresadern, José L. Medina-Franco, Karina Martínez-Mayorga, Thierry Langer, Karina Cuanalo-Contreras, Dimitris K. Agrafiotis
2009 J jnl
Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use.
J. Chem. Inf. Model.
Gary Tresadern, Dimitris K. Agrafiotis