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2020 – today
- 2024
[j18]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)- [j17]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) - [j16]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:
ACEGEN: Reinforcement Learning of Generative Chemical Agents for Drug Discovery. J. Chem. Inf. Model. 64(15): 5900-5911 (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)
Coauthor Index
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