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Gary Tresadern
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2020 – today
- 2024
- [j17]Morgan Thomas, Mazen Ahmad, Gary Tresadern, Gianni De Fabritiis:
PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models. J. Cheminformatics 16(1): 77 (2024) - [j16]David F. Hahn
, Vytautas Gapsys
, Bert L. de Groot
, David L. Mobley
, Gary Tresadern
:
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. J. Chem. Inf. Model. 64(13): 5063-5076 (2024) - [i1]Albert Bou, Morgan 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:
ACEGEN: Reinforcement learning of generative chemical agents for drug discovery. CoRR abs/2405.04657 (2024) - 2023
- [j15]Mary Pitman
, David F. Hahn
, Gary Tresadern
, David L. Mobley
:
To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough. J. Chem. Inf. Model. 63(6): 1776-1793 (2023) - [j14]Sridip Parui
, James C. Robertson
, Sandeep Somani, Gary Tresadern
, Cong Liu, Ken A. Dill
:
MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands. J. Chem. Inf. Model. 63(9): 2857-2865 (2023) - 2022
- [j13]Francesc Sabanés Zariquiey
, Edgar Jacoby, Ann Vos, Herman W. T. van Vlijmen
, Gary Tresadern
, Jeremy N. Harvey
:
Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery. J. Chem. Inf. Model. 62(3): 533-543 (2022) - [j12]Gary Tresadern
, Kanaka Tatikola, Javier Cabrera, Lingle Wang
, Robert Abel, Herman van Vlijmen
, Helena Geys:
The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions. J. Chem. Inf. Model. 62(3): 703-717 (2022) - [j11]Vytautas Gapsys
, David F. Hahn, Gary Tresadern
, David L. Mobley
, Markus Rampp, Bert L. de Groot
:
Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. J. Chem. Inf. Model. 62(5): 1172-1177 (2022) - [j10]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
:
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. J. Chem. Inf. Model. 62(23): 6094-6104 (2022) - 2021
- [j9]Yuriy Khalak
, Gary Tresadern
, Bert L. de Groot
, Vytautas Gapsys
:
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. J. Comput. Aided Mol. Des. 35(1): 49-61 (2021) - 2020
- [j8]Francesca Deflorian
, Laura Pérez-Benito
, Eelke B. Lenselink
, Miles Congreve
, Herman W. T. van Vlijmen
, Jonathan S. Mason, Chris de Graaf
, Gary Tresadern
:
Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation. J. Chem. Inf. Model. 60(11): 5563-5579 (2020)
2010 – 2019
- 2019
- [j7]Claudia Llinas del Torrent
, Nil Casajuana-Martin
, Leonardo Pardo
, Gary Tresadern
, Laura Pérez-Benito
:
Mechanisms Underlying Allosteric Molecular Switches of Metabotropic Glutamate Receptor 5. J. Chem. Inf. Model. 59(5): 2456-2466 (2019) - [j6]Angus Voice
, Gary Tresadern
, Herman van Vlijmen
, Adrian J. Mulholland
:
Limitations of Ligand-Only Approaches for Predicting the Reactivity of Covalent Inhibitors. J. Chem. Inf. Model. 59(10): 4220-4227 (2019) - 2018
- [j5]Laura Pérez-Benito
, Andrew Henry, Minos-Timotheos Matsoukas
, Laura Lopez, Daniel Pulido
, Miriam Royo, Arnau Cordomí, Gary Tresadern
, Leonardo Pardo
:
The size matters? A computational tool to design bivalent ligands. Bioinform. 34(22): 3857-3863 (2018) - 2017
- [j4]Gary Tresadern
, Andrés A. Trabanco
, Laura Pérez-Benito
, John P. Overington
, Herman W. T. van Vlijmen, Gerard J. P. van Westen
:
Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling. J. Chem. Inf. Model. 57(12): 2976-2985 (2017) - 2016
- [j3]Myriam Ciordia, Laura Pérez-Benito
, Francisca Delgado, Andrés A. Trabanco
, Gary Tresadern
:
Application of Free Energy Perturbation for the Design of BACE1 Inhibitors. J. Chem. Inf. Model. 56(9): 1856-1871 (2016) - 2012
- [j2]Thomas Scior, Andreas Bender, Gary Tresadern
, José L. Medina-Franco
, Karina Martínez-Mayorga, Thierry Langer
, Karina Cuanalo-Contreras, Dimitris K. Agrafiotis
:
Recognizing Pitfalls in Virtual Screening: A Critical Review. J. Chem. Inf. Model. 52(4): 867-881 (2012)
2000 – 2009
- 2009
- [j1]Gary Tresadern
, Dimitris K. Agrafiotis
:
Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use. J. Chem. Inf. Model. 49(12): 2786-2800 (2009)
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last updated on 2024-08-23 18:35 CEST by the dblp team
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