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2020 – today
- 2024
[j16]Morgan C. Thomas, Noel M. O'Boyle, Andreas Bender, Chris de Graaf:
MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design. J. Cheminformatics 16(1): 64 (2024)- 2023
- [j15]Georgi K. Kanev, Yaran Zhang, Albert J. Kooistra
, Andreas Bender, Rob Leurs, David Bailey, Thomas Würdinger, Chris de Graaf, Iwan J. P. de Esch, Bart A. Westerman:
Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks. PLoS Comput. Biol. 19(9) (2023) - 2022
- [j14]Morgan C. Thomas, Noel M. O'Boyle, Andreas Bender, Chris de Graaf:
Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation. J. Cheminformatics 14(1): 68 (2022) - [j13]Alessandro Nicoli, Andreas Dunkel, Toni Giorgino, Chris de Graaf, Antonella Di Pizio:
Classification Model for the Second Extracellular Loop of Class A GPCRs. J. Chem. Inf. Model. 62(3): 511-522 (2022) - [i1]Morgan C. Thomas, Noel M. O'Boyle, Andreas Bender, Chris de Graaf:
Re-evaluating sample efficiency in de novo molecule generation. CoRR abs/2212.01385 (2022) - 2021
- [j12]Morgan C. Thomas, Robert T. Smith, Noel M. O'Boyle, Chris de Graaf, Andreas Bender:
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study. J. Cheminformatics 13(1): 39 (2021) - [j11]Georgi K. Kanev, Chris de Graaf, Bart A. Westerman, Iwan J. P. de Esch, Albert J. Kooistra:
KLIFS: an overhaul after the first 5 years of supporting kinase research. Nucleic Acids Res. 49(Database-Issue): D562-D569 (2021) - 2020
- [j10]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
- [j9]Giulio Mattedi, Francesca Deflorian, Jonathan S. Mason, Chris de Graaf, Francesco L. Gervasio:
Understanding Ligand Binding Selectivity in a Prototypical GPCR Family. J. Chem. Inf. Model. 59(6): 2830-2836 (2019) - 2017
- [j8]Ross McGuire, Stefan Verhoeven, Márton Vass, Gerrit Vriend, Iwan J. P. de Esch, Scott J. Lusher, Rob Leurs, Lars Ridder, Albert J. Kooistra, Tina Ritschel, Chris de Graaf:
3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. J. Chem. Inf. Model. 57(2): 115-121 (2017) - 2016
- [j7]Albert J. Kooistra, Georgi K. Kanev, Oscar P. J. van Linden, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf:
KLIFS: a structural kinase-ligand interaction database. Nucleic Acids Res. 44(Database-Issue): 365-371 (2016) - 2015
- [j6]Oscar Méndez-Lucio, Albert J. Kooistra, Chris de Graaf, Andreas Bender, José L. Medina-Franco:
Analyzing Multitarget Activity Landscapes Using Protein-Ligand Interaction Fingerprints: Interaction Cliffs. J. Chem. Inf. Model. 55(2): 251-262 (2015) - [j5]Sabine Schultes, Albert J. Kooistra, Henry F. Vischer, Saskia Nijmeijer, Eric E. J. Haaksma, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf:
Combinatorial Consensus Scoring for Ligand-Based Virtual Fragment Screening: A Comparative Case Study for Serotonin 5-HT3A, Histamine H1, and Histamine H4 Receptors. J. Chem. Inf. Model. 55(5): 1030-1044 (2015) - [j4]Albert J. Kooistra, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf:
Structure-Based Prediction of G-Protein-Coupled Receptor Ligand Function: A β-Adrenoceptor Case Study. J. Chem. Inf. Model. 55(5): 1045-1061 (2015) - 2012
- [j3]Francesco Sirci, Enade P. Istyastono, Henry F. Vischer, Albert J. Kooistra, Saskia Nijmeijer, Martien Kuijer, Maikel Wijtmans, Raimund Mannhold, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf:
Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints. J. Chem. Inf. Model. 52(12): 3308-3324 (2012) - 2011
- [j2]Marijn P. A. Sanders, Stefan Verhoeven, Chris de Graaf, Luc Roumen, Bas Vroling, Sander B. Nabuurs, Jacob de Vlieg, Jan P. G. Klomp:
Snooker: A Structure-Based Pharmacophore Generation Tool Applied to Class A GPCRs. J. Chem. Inf. Model. 51(9): 2277-2292 (2011) - 2010
- [j1]Albert J. Kooistra, Thomas W. Binsl, Johannes H. G. M. van Beek, Chris de Graaf, Jaap Heringa:
Electron Density Fingerprints (EDprints): Virtual Screening Using Assembled Information of Electron Density. J. Chem. Inf. Model. 50(10): 1772-1780 (2010)
Coauthor Index
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