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ORCIDBibTeX records: Herman van Vlijmen
@article{DBLP:journals/qmi/VarsamopoulosPEVMVDTR24,
author = {Savvas Varsamopoulos and
Evan Philip and
Vincent E. Elfving and
Herman W. T. van Vlijmen and
Sairam Menon and
Ann Vos and
Natalia Dyubankova and
Bert Torfs and
Anthony Rowe},
title = {Quantum extremal learning},
journal = {Quantum Mach. Intell.},
volume = {6},
number = {2},
pages = {42},
year = {2024},
url = {https://doi.org/10.1007/s42484-024-00176-x},
doi = {10.1007/S42484-024-00176-X},
timestamp = {Mon, 05 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/qmi/VarsamopoulosPEVMVDTR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/LiuYVIW23,
author = {Xuhan Liu and
Kai Ye and
Herman W. T. van Vlijmen and
Adriaan P. IJzerman and
Gerard J. P. van Westen},
title = {DrugEx v3: scaffold-constrained drug design with graph transformer-based
reinforcement learning},
journal = {J. Cheminformatics},
volume = {15},
number = {1},
pages = {24},
year = {2023},
url = {https://doi.org/10.1186/s13321-023-00694-z},
doi = {10.1186/S13321-023-00694-Z},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/LiuYVIW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ZariquieyJVVTH22,
author = {Francesc Saban{\'{e}}s Zariquiey and
Edgar Jacoby and
Ann Vos and
Herman W. T. van Vlijmen and
Gary Tresadern and
Jeremy N. Harvey},
title = {Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the
Perspective of Docking Virtual Screening Applications for Drug Discovery},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {3},
pages = {533--543},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.1c01164},
doi = {10.1021/ACS.JCIM.1C01164},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/ZariquieyJVVTH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/TresadernTCWAVG22,
author = {Gary Tresadern and
Kanaka Tatikola and
Javier Cabrera and
Lingle Wang and
Robert Abel and
Herman van Vlijmen and
Helena Geys},
title = {The Impact of Experimental and Calculated Error on the Performance
of Affinity Predictions},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {3},
pages = {703--717},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.1c01214},
doi = {10.1021/ACS.JCIM.1C01214},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/TresadernTCWAVG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2205-02807,
author = {Savvas Varsamopoulos and
Evan Philip and
Herman W. T. van Vlijmen and
Sairam Menon and
Ann Vos and
Natalia Dyubankova and
Bert Torfs and
Anthony Rowe and
Vincent E. Elfving},
title = {Quantum Extremal Learning},
journal = {CoRR},
volume = {abs/2205.02807},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2205.02807},
doi = {10.48550/ARXIV.2205.02807},
eprinttype = {arXiv},
eprint = {2205.02807},
timestamp = {Mon, 22 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2205-02807.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/LiuYVEIW21,
author = {Xuhan Liu and
Kai Ye and
Herman W. T. van Vlijmen and
Michael T. M. Emmerich and
Adriaan P. IJzerman and
Gerard J. P. van Westen},
title = {DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective
reinforcement learning in polypharmacology},
journal = {J. Cheminformatics},
volume = {13},
number = {1},
pages = {85},
year = {2021},
url = {https://doi.org/10.1186/s13321-021-00561-9},
doi = {10.1186/S13321-021-00561-9},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/LiuYVEIW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dint/VlijmenMWFBRKSM20,
author = {Herman van Vlijmen and
Albert Mons and
Arne Waalkens and
Wouter Franke and
Arie Baak and
Gerbrand Ruiter and
Christine R. Kirkpatrick and
Luiz Olavo Bonino da Silva Santos and
Bert Meerman and
Renger Jellema and
Derk L. Arts and
Martijn G. Kersloot and
Sebastiaan L. Knijnenburg and
Scott J. Lusher and
Rudi Verbeeck and
Jean{-}Marc Neefs},
title = {The Need of Industry to Go {FAIR}},
journal = {Data Intell.},
volume = {2},
number = {1-2},
pages = {276--284},
year = {2020},
url = {https://doi.org/10.1162/dint\_a\_00050},
doi = {10.1162/DINT\_A\_00050},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dint/VlijmenMWFBRKSM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/BurggraaffVIW20,
author = {Lindsey Burggraaff and
Herman W. T. van Vlijmen and
Adriaan P. IJzerman and
Gerard J. P. van Westen},
title = {Quantitative prediction of selectivity between the A\({}_{\mbox{1}}\)
and A\({}_{\mbox{2A}}\) adenosine receptors},
journal = {J. Cheminformatics},
volume = {12},
number = {1},
pages = {33},
year = {2020},
url = {https://doi.org/10.1186/s13321-020-00438-3},
doi = {10.1186/S13321-020-00438-3},
timestamp = {Fri, 14 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/BurggraaffVIW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BurggraaffLJEBG20,
author = {Lindsey Burggraaff and
Eelke B. Lenselink and
Willem Jespers and
Jesper E. van Engelen and
Brandon J. Bongers and
Marina Gorostiola Gonz{\'{a}}lez and
Rongfang Liu and
Holger H. Hoos and
Herman W. T. van Vlijmen and
Adriaan P. IJzerman and
Gerard J. P. van Westen},
title = {Successive Statistical and Structure-Based Modeling to Identify Chemically
Novel Kinase Inhibitors},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {9},
pages = {4283--4295},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.9b01204},
doi = {10.1021/ACS.JCIM.9B01204},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BurggraaffLJEBG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BurggraaffVLVIW20,
author = {Lindsey Burggraaff and
Amber van Veen and
Chi Chung Lam and
Herman W. T. van Vlijmen and
Adriaan P. IJzerman and
Gerard J. P. van Westen},
title = {Annotation of Allosteric Compounds to Enhance Bioactivity Modeling
for Class {A} GPCRs},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {10},
pages = {4664--4672},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.0c00695},
doi = {10.1021/ACS.JCIM.0C00695},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BurggraaffVLVIW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/GoossensWLVCW20,
author = {Kenneth Goossens and
Berthold Wroblowski and
Cassiano Langini and
Herman van Vlijmen and
Amedeo Caflisch and
Hans De Winter},
title = {Assessment of the Fragment Docking Program {SEED}},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {10},
pages = {4881--4893},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.0c00556},
doi = {10.1021/ACS.JCIM.0C00556},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/GoossensWLVCW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/DeflorianPLCVMG20,
author = {Francesca Deflorian and
Laura P{\'{e}}rez{-}Benito and
Eelke B. Lenselink and
Miles Congreve and
Herman W. T. van Vlijmen and
Jonathan S. Mason and
Chris de Graaf and
Gary Tresadern},
title = {Accurate Prediction of {GPCR} Ligand Binding Affinity with Free Energy
Perturbation},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {11},
pages = {5563--5579},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.0c00449},
doi = {10.1021/ACS.JCIM.0C00449},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/DeflorianPLCVMG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/BurggraaffOGPGV19,
author = {Lindsey Burggraaff and
Paul Oranje and
Robin Gouka and
Pieter van der Pijl and
Marian Geldof and
Herman W. T. van Vlijmen and
Adriaan P. IJzerman and
Gerard J. P. van Westen},
title = {Identification of novel small molecule inhibitors for solute carrier
{SGLT1} using proteochemometric modeling},
journal = {J. Cheminformatics},
volume = {11},
number = {1},
pages = {15:1--15:10},
year = {2019},
url = {https://doi.org/10.1186/s13321-019-0337-8},
doi = {10.1186/S13321-019-0337-8},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/BurggraaffOGPGV19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/LiuYVIW19,
author = {Xuhan Liu and
Kai Ye and
Herman W. T. van Vlijmen and
Adriaan P. IJzerman and
Gerard J. P. van Westen},
title = {An exploration strategy improves the diversity of de novo ligands
using deep reinforcement learning: a case for the adenosine {A2A}
receptor},
journal = {J. Cheminformatics},
volume = {11},
number = {1},
pages = {35:1--35:16},
year = {2019},
url = {https://doi.org/10.1186/s13321-019-0355-6},
doi = {10.1186/S13321-019-0355-6},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/LiuYVIW19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SydowBSVIWV19,
author = {Dominique Sydow and
Lindsey Burggraaff and
Angelika Szengel and
Herman W. T. van Vlijmen and
Adriaan P. IJzerman and
Gerard J. P. van Westen and
Andrea Volkamer},
title = {Advances and Challenges in Computational Target Prediction},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {5},
pages = {1728--1742},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.8b00832},
doi = {10.1021/ACS.JCIM.8B00832},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/SydowBSVIWV19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/VoiceTVM19,
author = {Angus Voice and
Gary Tresadern and
Herman van Vlijmen and
Adrian J. Mulholland},
title = {Limitations of Ligand-Only Approaches for Predicting the Reactivity
of Covalent Inhibitors},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {10},
pages = {4220--4227},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.9b00404},
doi = {10.1021/ACS.JCIM.9B00404},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/VoiceTVM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/GhanakotaVSB18,
author = {Phani Ghanakota and
Herman van Vlijmen and
Woody Sherman and
Thijs Beuming},
title = {Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots
at Protein-Protein Interaction Interfaces},
journal = {J. Chem. Inf. Model.},
volume = {58},
number = {4},
pages = {784--793},
year = {2018},
url = {https://doi.org/10.1021/acs.jcim.7b00487},
doi = {10.1021/ACS.JCIM.7B00487},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/GhanakotaVSB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VlijmenDM17,
author = {Herman van Vlijmen and
Renee L. DesJarlais and
Tara Mirzadegan},
title = {Computational chemistry at Janssen},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {267--273},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9998-9},
doi = {10.1007/S10822-016-9998-9},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VlijmenDM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/LenselinkDBPVKI17,
author = {Eelke B. Lenselink and
Niels ten Dijke and
Brandon J. Bongers and
George Papadatos and
Herman W. T. van Vlijmen and
Wojtek Kowalczyk and
Adriaan P. IJzerman and
Gerard J. P. van Westen},
title = {Beyond the hype: deep neural networks outperform established methods
using a ChEMBL bioactivity benchmark set},
journal = {J. Cheminformatics},
volume = {9},
number = {1},
pages = {45},
year = {2017},
url = {https://doi.org/10.1186/s13321-017-0232-0},
doi = {10.1186/S13321-017-0232-0},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/LenselinkDBPVKI17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/TresadernTPOVW17,
author = {Gary Tresadern and
Andr{\'{e}}s A. Trabanco and
Laura P{\'{e}}rez{-}Benito and
John P. Overington and
Herman W. T. van Vlijmen and
Gerard J. P. van Westen},
title = {Identification of Allosteric Modulators of Metabotropic Glutamate
7 Receptor Using Proteochemometric Modeling},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {12},
pages = {2976--2985},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.7b00338},
doi = {10.1021/ACS.JCIM.7B00338},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/TresadernTPOVW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LenselinkBVMSVI16,
author = {Eelke B. Lenselink and
Thijs Beuming and
Corine van Veen and
Arnault Massink and
Woody Sherman and
Herman W. T. van Vlijmen and
Adriaan P. IJzerman},
title = {In search of novel ligands using a structure-based approach: a case
study on the adenosine {A2A} receptor},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {10},
pages = {863--874},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9963-7},
doi = {10.1007/S10822-016-9963-7},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LenselinkBVMSVI16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SherborneSCCDDL16,
author = {Bradley Sherborne and
Veerabahu Shanmugasundaram and
Alan C. Cheng and
Clara D. Christ and
Renee L. DesJarlais and
Jos{\'{e}} S. Duca and
Richard A. Lewis and
Deborah A. Loughney and
Eric S. Manas and
Georgia B. McGaughey and
Catherine E. Peishoff and
Herman van Vlijmen},
title = {Collaborating to improve the use of free-energy and other quantitative
methods in drug discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {12},
pages = {1139--1141},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9996-y},
doi = {10.1007/S10822-016-9996-Y},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SherborneSCCDDL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LenselinkJVIW16,
author = {Eelke B. Lenselink and
Willem Jespers and
Herman W. T. van Vlijmen and
Adriaan P. IJzerman and
Gerard J. P. van Westen},
title = {Interacting with GPCRs: Using Interaction Fingerprints for Virtual
Screening},
journal = {J. Chem. Inf. Model.},
volume = {56},
number = {10},
pages = {2053--2060},
year = {2016},
url = {https://doi.org/10.1021/acs.jcim.6b00314},
doi = {10.1021/ACS.JCIM.6B00314},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/LenselinkJVIW16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BorghtTWCVRVA15,
author = {Koen Van der Borght and
Kim Thys and
Yves Wetzels and
Lieven Clement and
Bie M. P. Verbist and
Joke Reumers and
Herman van Vlijmen and
Jeroen Aerssens},
title = {{QQ-SNV:} single nucleotide variant detection at low frequency by
comparing the quality quantiles},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {379:1--379:14},
year = {2015},
url = {https://doi.org/10.1186/s12859-015-0812-9},
doi = {10.1186/S12859-015-0812-9},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BorghtTWCVRVA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BorghtVV14,
author = {Koen Van der Borght and
Geert Verbeke and
Herman van Vlijmen},
title = {Multi-model inference using mixed effects from a linear regression
based genetic algorithm},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {88},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-88},
doi = {10.1186/1471-2105-15-88},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BorghtVV14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LenselinkBSVI14,
author = {Eelke B. Lenselink and
Thijs Beuming and
Woody Sherman and
Herman W. T. van Vlijmen and
Adriaan P. IJzerman},
title = {Selecting an Optimal Number of Binding Site Waters To Improve Virtual
Screening Enrichments Against the Adenosine A\({}_{\mbox{2A}}\) Receptor},
journal = {J. Chem. Inf. Model.},
volume = {54},
number = {6},
pages = {1737--1746},
year = {2014},
url = {https://doi.org/10.1021/ci5000455},
doi = {10.1021/CI5000455},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/LenselinkBSVI14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/WestenSWIVB13,
author = {Gerard J. P. van Westen and
Remco F. Swier and
J{\"{o}}rg K. Wegner and
Adriaan P. IJzerman and
Herman W. T. van Vlijmen and
Andreas Bender},
title = {Benchmarking of protein descriptor sets in proteochemometric modeling
(part 1): comparative study of 13 amino acid descriptor sets},
journal = {J. Cheminformatics},
volume = {5},
pages = {41},
year = {2013},
url = {https://doi.org/10.1186/1758-2946-5-41},
doi = {10.1186/1758-2946-5-41},
timestamp = {Tue, 31 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/WestenSWIVB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/WestenSCWOIVB13,
author = {Gerard J. P. van Westen and
Remco F. Swier and
Isidro Cortes{-}Ciriano and
J{\"{o}}rg K. Wegner and
John P. Overington and
Adriaan P. IJzerman and
Herman W. T. van Vlijmen and
Andreas Bender},
title = {Benchmarking of protein descriptor sets in proteochemometric modeling
(part 2): modeling performance of 13 amino acid descriptor sets},
journal = {J. Cheminformatics},
volume = {5},
pages = {42},
year = {2013},
url = {https://doi.org/10.1186/1758-2946-5-42},
doi = {10.1186/1758-2946-5-42},
timestamp = {Tue, 31 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/WestenSCWOIVB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WestenHWIVB13,
author = {Gerard J. P. van Westen and
Alwin Hendriks and
J{\"{o}}rg K. Wegner and
Adriaan P. IJzerman and
Herman W. T. van Vlijmen and
Andreas Bender},
title = {Significantly Improved {HIV} Inhibitor Efficacy Prediction Employing
Proteochemometric Models Generated From Antivirogram Data},
journal = {PLoS Comput. Biol.},
volume = {9},
number = {2},
year = {2013},
url = {https://doi.org/10.1371/journal.pcbi.1002899},
doi = {10.1371/JOURNAL.PCBI.1002899},
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