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ORCIDHerman van Vlijmen
Person information
- affiliation: Leiden University, The Netherlands
- affiliation (former): Discovery Sciences, Janssen Research and Development, Beerse, Belgium
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Journal Articles
- 2024
[j35]Savvas Varsamopoulos, Evan Philip
, Vincent E. Elfving, Herman W. T. van Vlijmen, Sairam Menon, Ann Vos, Natalia Dyubankova, Bert Torfs, Anthony Rowe:
Quantum extremal learning. Quantum Mach. Intell. 6(2): 42 (2024)- 2023
- [j34]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): 24 (2023) - 2022
- [j33]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) - [j32]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) - 2021
- [j31]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): 85 (2021) - 2020
- [j30]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, Sebastiaan L. Knijnenburg, Scott J. Lusher, Rudi Verbeeck, Jean-Marc Neefs:
The Need of Industry to Go FAIR. Data Intell. 2(1-2): 276-284 (2020) - [j29]Lindsey Burggraaff, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen:
Quantitative prediction of selectivity between the A1 and A2A adenosine receptors. J. Cheminformatics 12(1): 33 (2020) - [j28]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): 4283-4295 (2020) - [j27]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): 4664-4672 (2020) - [j26]Kenneth Goossens, Berthold Wroblowski, Cassiano Langini, Herman van Vlijmen, Amedeo Caflisch, Hans De Winter:
Assessment of the Fragment Docking Program SEED. J. Chem. Inf. Model. 60(10): 4881-4893 (2020) - [j25]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) - 2019
- [j24]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): 15:1-15:10 (2019) - [j23]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): 35:1-35:16 (2019) - [j22]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): 1728-1742 (2019) - [j21]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
- [j20]Phani Ghanakota, Herman van Vlijmen, Woody Sherman, Thijs Beuming:
Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces. J. Chem. Inf. Model. 58(4): 784-793 (2018) - 2017
- [j19]Herman van Vlijmen, Renee L. DesJarlais, Tara Mirzadegan:
Computational chemistry at Janssen. J. Comput. Aided Mol. Des. 31(3): 267-273 (2017) - [j18]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): 45 (2017) - [j17]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
- [j16]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): 863-874 (2016) - [j15]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:
Collaborating to improve the use of free-energy and other quantitative methods in drug discovery. J. Comput. Aided Mol. Des. 30(12): 1139-1141 (2016) - [j14]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): 2053-2060 (2016) - 2015
- [j13]Koen Van der Borght, Kim Thys, Yves Wetzels, Lieven Clement, Bie M. P. Verbist, Joke Reumers, Herman van Vlijmen, Jeroen Aerssens:
QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles. BMC Bioinform. 16: 379:1-379:14 (2015) - 2014
- [j12]Koen Van der Borght, Geert Verbeke, Herman van Vlijmen:
Multi-model inference using mixed effects from a linear regression based genetic algorithm. BMC Bioinform. 15: 88 (2014) - [j11]Eelke B. Lenselink, Thijs Beuming, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman:
Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A2A Receptor. J. Chem. Inf. Model. 54(6): 1737-1746 (2014) - 2013
- [j10]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: 41 (2013) - [j9]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: 42 (2013) - [j8]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) - 2012
- [j7]Jörg K. Wegner, Aaron D. Sterling, Rajarshi Guha, Andreas Bender, Jean-Loup Faulon, Janna Hastings, Noel M. O'Boyle, John P. Overington, Herman van Vlijmen, Egon L. Willighagen:
Cheminformatics. Commun. ACM 55(11): 65-75 (2012) - 2011
- [j6]Koen Van der Borght, Elke Van Craenenbroeck, Pierre Lecocq, Margriet Van Houtte, Barbara Van Kerckhove, Lee Bacheler, Geert Verbeke, Herman van Vlijmen:
Cross-validated stepwise regression for identification of novel non-nucleoside reverse transcriptase inhibitor resistance associated mutations. BMC Bioinform. 12: 386 (2011) - 2010
- [j5]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: 316 (2010) - [j4]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): 3 (2010) - 2002
- [j3]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, Steven P. Adams:
3D QSAR (COMFA) of a series of potent and highly selective VLA-4 antagonists. J. Comput. Aided Mol. Des. 16(3): 201-211 (2002) - 1989
- [j2]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): 165-174 (1989) - 1988
- [j1]Adriaan P. IJzerman, Herman W. T. van Vlijmen:
A molecular graphics study exploring a putative ligand binding site of theβ-adrenoceptor. J. Comput. Aided Mol. Des. 2(1): 43-53 (1988)
Conference and Workshop Papers
- 2012
- [c1]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: 12-24
Informal and Other Publications
- 2022
- [i1]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 abs/2205.02807 (2022)
Coauthor Index
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