Gary Tresadern

According to our database, Gary Tresadern authored at least 18 papers between 2009 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models.

Morgan Thomas, Mazen Ahmad, Gary Tresadern, Gianni De Fabritiis

J. Cheminformatics, December, 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

ACEGEN: Reinforcement Learning of Generative Chemical Agents for Drug Discovery.

Albert Bou, Morgan Thomas, Sebastian Dittert, Carles Navarro, Maciej Majewski, Ye Wang, Shivam Patel, Gary Tresadern, Mazen Ahmad, Vincent Moens, Woody Sherman, Simone Sciabola, Gianni De Fabritiis

J. Chem. Inf. Model., 2024

2023

MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands.

Sridip Parui, James C. Robertson, Sandeep Somani, Gary Tresadern, Cong Liu, Ken A. Dill

J. Chem. Inf. Model., May, 2023

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., March, 2023

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

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

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

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, Arjun Narayanan, Christina E. M. Schindler, William C. Swope, Pieter J. in 't Veld, Jeffrey Wagner, Bai Xue, Gary Tresadern

J. Chem. Inf. Model., 2022

2021

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

2020

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

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

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

2018

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

2017

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., December, 2017

2016

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

2012

Recognizing Pitfalls in Virtual Screening: A Critical Review.

Thomas Scior, Andreas Bender, Gary Tresadern, José L. Medina-Franco, Karina Martínez-Mayorga, Thierry Langer, Karina Cuanalo-Contreras, Dimitris K. Agrafiotis

J. Chem. Inf. Model., 2012

2009

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