Herman W. T. van Vlijmen

Publication Activity (10 Years)

Years Active: 1988-2023
Publications (10 Years): 15

Top Topics

Reinforcement Learning

Comparative Study

Chemical Compounds

Top Venues

J. Cheminformatics

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

Publications

Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning. J. Cheminformatics 15 (1) (2023)
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) (2022)
Savvas Varsamopoulos, Evan Philip, Herman W. T. van Vlijmen, Sairam Menon, Ann Vos, Natalia Dyubankova, Bert Torfs, Anthony Rowe, Vincent E. Elfving
Quantum Extremal Learning. CoRR (2022)
Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Adriaan P. IJzerman, Gerard J. P. van Westen
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology. J. Cheminformatics 13 (1) (2021)
Lindsey Burggraaff, Amber van Veen, Chi Chung Lam, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. J. Chem. Inf. Model. 60 (10) (2020)
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) (2020)
Lindsey Burggraaff, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
adenosine receptors. J. Cheminformatics 12 (1) (2020)
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
Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. J. Chem. Inf. Model. 60 (9) (2020)
Dominique Sydow, Lindsey Burggraaff, Angelika Szengel, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen, Andrea Volkamer
Advances and Challenges in Computational Target Prediction. J. Chem. Inf. Model. 59 (5) (2019)
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
Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling. J. Cheminformatics 11 (1) (2019)
Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor. J. Cheminformatics 11 (1) (2019)
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) (2017)
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
Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set. J. Cheminformatics 9 (1) (2017)
Eelke B. Lenselink, Willem Jespers, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening. J. Chem. Inf. Model. 56 (10) (2016)
Eelke B. Lenselink, Thijs Beuming, Corine van Veen, Arnault Massink, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman
In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor. J. Comput. Aided Mol. Des. 30 (10) (2016)
Eelke B. Lenselink, Thijs Beuming, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman
Receptor. J. Chem. Inf. Model. 54 (6) (2014)
Gerard J. P. van Westen, Remco F. Swier, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. J. Cheminformatics 5 (2013)
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
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. J. Cheminformatics 5 (2013)
Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data. PLoS Comput. Biol. 9 (2) (2013)
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
Using Multiobjective Optimization and Energy Minimization to Design an Isoform-Selective Ligand of the 14-3-3 Protein. ISoLA (2) (2012)
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
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. BMC Bioinform. 11 (2010)
Gerard J. P. van Westen, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
Molecular bioactivity extrapolation to novel targets by support vector machines. J. Cheminformatics 2 (S-1) (2010)
Herman W. T. van Vlijmen, Adriaan P. IJzerman
Molecular modeling of a putative antagonist binding site on helix III of the β-adrenoceptor. J. Comput. Aided Mol. Des. 3 (2) (1989)
Adriaan P. IJzerman, Herman W. T. van Vlijmen
-adrenoceptor. J. Comput. Aided Mol. Des. 2 (1) (1988)