A molecular graphics study exploring a putative ligand binding site of theβ-adrenoceptor. - Adriaan P. IJzerman; Herman W. T. van Vlijmen (J. Comput. Aided Mol. Des., 1988)

Molecular modeling of a putative antagonist binding site on helix III of the β-adrenoceptor. - Herman W. T. van Vlijmen; Adriaan P. IJzerman (J. Comput. Aided Mol. Des., 1989)

3D QSAR (COMFA) of a series of potent and highly selective VLA-4 antagonists. - Juswinder Singh; Herman van Vlijmen; Wen-Cherng Lee; Yusheng Liao; Ko-Chung Lin; Humayun Ateeq; Julio Cuervo; Craig Zimmerman; Charles Hammond; Michael Karpusas; Rex Palmer; Tapan Chattopadhyay; et al. (J. Comput. Aided Mol. Des., 2002)

A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. - Eelke van der Horst; Julio E. Peironcely; Adriaan P. IJzerman; Margot W. Beukers; Jonathan Robert Lane; Herman W. T. van Vlijmen; Michael T. M. Emmerich; Yasushi Okuno; Andreas Bender 002 (BMC Bioinform., 2010)

Molecular bioactivity extrapolation to novel targets by support vector machines. - Gerard J. P. van Westen; Jörg K. Wegner; Adriaan P. IJzerman; Herman W. T. van Vlijmen; Andreas Bender 002 (J. Cheminformatics, 2010)

Cross-validated stepwise regression for identification of novel non-nucleoside reverse transcriptase inhibitor resistance associated mutations. - Koen Van der Borght; Elke Van Craenenbroeck; Pierre Lecocq; Margriet Van Houtte; Barbara Van Kerckhove; Lee Bacheler; Geert Verbeke; Herman van Vlijmen (BMC Bioinform., 2011)

Using Multiobjective Optimization and Energy Minimization to Design an Isoform-Selective Ligand of the 14-3-3 Protein. - Hernando Sanchez-Faddeev; Michael T. M. Emmerich; Fons J. Verbeek; Andrew H. Henry; Simon Grimshaw; Herman P. Spaink; Herman W. T. van Vlijmen; Andreas Bender 002 (ISoLA (2), 2012)

Cheminformatics. - Jörg K. Wegner; Aaron D. Sterling; Rajarshi Guha; Andreas Bender 002; Jean-Loup Faulon; Janna Hastings; Noel M. O'Boyle; John P. Overington; Herman van Vlijmen; Egon L. Willighagen (Commun. ACM, 2012)

Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. - Gerard J. P. van Westen; Remco F. Swier; Isidro Cortes-Ciriano; Jörg K. Wegner; John P. Overington; Adriaan P. IJzerman; Herman W. T. van Vlijmen; Andreas Bender 002 (J. Cheminformatics, 2013)

Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. - Gerard J. P. van Westen; Remco F. Swier; Jörg K. Wegner; Adriaan P. IJzerman; Herman W. T. van Vlijmen; Andreas Bender 002 (J. Cheminformatics, 2013)

Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data. - Gerard J. P. van Westen; Alwin Hendriks; Jörg K. Wegner; Adriaan P. IJzerman; Herman W. T. van Vlijmen; Andreas Bender 002 (PLoS Comput. Biol., 2013)

Multi-model inference using mixed effects from a linear regression based genetic algorithm. - Koen Van der Borght; Geert Verbeke; Herman van Vlijmen (BMC Bioinform., 2014)

Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A2A Receptor. - Eelke B. Lenselink; Thijs Beuming; Woody Sherman; Herman W. T. van Vlijmen; Adriaan P. IJzerman (J. Chem. Inf. Model., 2014)

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles. - Koen Van der Borght; Kim Thys; Yves Wetzels; Lieven Clement; Bie M. P. Verbist; Joke Reumers; Herman van Vlijmen; Jeroen Aerssens (BMC Bioinform., 2015)

In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor. - Eelke B. Lenselink; Thijs Beuming; Corine van Veen; Arnault Massink; Woody Sherman; Herman W. T. van Vlijmen; Adriaan P. IJzerman (J. Comput. Aided Mol. Des., 2016)

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery. - Bradley Sherborne; Veerabahu Shanmugasundaram; Alan C. Cheng; Clara D. Christ; Renee L. DesJarlais; José S. Duca; Richard A. Lewis; Deborah A. Loughney; Eric S. Manas; Georgia B. McGaughey; Catherine E. Peishoff; Herman van Vlijmen (J. Comput. Aided Mol. Des., 2016)

Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening. - Eelke B. Lenselink; Willem Jespers; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Chem. Inf. Model., 2016)

Computational chemistry at Janssen. - Herman van Vlijmen; Renee L. DesJarlais; Tara Mirzadegan (J. Comput. Aided Mol. Des., 2017)

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set. - Eelke B. Lenselink; Niels ten Dijke; Brandon J. Bongers; George Papadatos; Herman W. T. van Vlijmen; Wojtek Kowalczyk; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 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., 2017)

Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces. - Phani Ghanakota; Herman van Vlijmen; Woody Sherman; Thijs Beuming (J. Chem. Inf. Model., 2018)

Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling. - Lindsey Burggraaff; Paul Oranje; Robin Gouka; Pieter van der Pijl; Marian Geldof; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2019)

An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor. - Xuhan Liu; Kai Ye 001; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2019)

Advances and Challenges in Computational Target Prediction. - Dominique Sydow; Lindsey Burggraaff; Angelika Szengel; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen; Andrea Volkamer (J. Chem. Inf. Model., 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)

The Need of Industry to Go FAIR. - Herman van Vlijmen; Albert Mons; Arne Waalkens; Wouter Franke; Arie Baak; Gerbrand Ruiter; Christine R. Kirkpatrick; Luiz Olavo Bonino da Silva Santos; Bert Meerman; Renger Jellema; Derk L. Arts; Martijn G. Kersloot; et al. (Data Intell., 2020)

Quantitative prediction of selectivity between the A1 and A2A adenosine receptors. - Lindsey Burggraaff; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2020)

Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. - Lindsey Burggraaff; Eelke B. Lenselink; Willem Jespers; Jesper E. van Engelen; Brandon J. Bongers; Marina Gorostiola González; Rongfang Liu; Holger H. Hoos; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Chem. Inf. Model., 2020)

Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. - Lindsey Burggraaff; Amber van Veen; Chi Chung Lam; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Chem. Inf. Model., 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)

Assessment of the Fragment Docking Program SEED. - Kenneth Goossens; Berthold Wroblowski; Cassiano Langini; Herman van Vlijmen; Amedeo Caflisch; Hans De Winter (J. Chem. Inf. Model., 2020)

DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology. - Xuhan Liu; Kai Ye 001; Herman W. T. van Vlijmen; Michael T. M. Emmerich; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2021)

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)

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)

DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning. - Xuhan Liu; Kai Ye 001; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2023)

Quantum extremal learning. - Savvas Varsamopoulos; Evan Philip; Vincent E. Elfving; Herman W. T. van Vlijmen; Sairam Menon; Ann Vos; Natalia Dyubankova; Bert Torfs; Anthony Rowe 002 (Quantum Mach. Intell., 2024)