Advances and Challenges in Computational Target Prediction
Sydow, Dominique, Burggraaff, Lindsey, Szengel, Angelika, van Vlijmen, Herman W. T, IJzerman, Adriaan P, van Westen, Gerard J. P, Volkamer, Andrea
Published in Journal of chemical information and modeling (28.05.2019)
Published in Journal of chemical information and modeling (28.05.2019)
Get full text
Journal Article
Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set
Lenselink, Eelke B., ten Dijke, Niels, Bongers, Brandon, Papadatos, George, van Vlijmen, Herman W. T., Kowalczyk, Wojtek, IJzerman, Adriaan P., van Westen, Gerard J. P.
Published in Journal of cheminformatics (14.08.2017)
Published in Journal of cheminformatics (14.08.2017)
Get full text
Journal Article
Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation
Deflorian, Francesca, Perez-Benito, Laura, Lenselink, Eelke B, Congreve, Miles, van Vlijmen, Herman W. T, Mason, Jonathan S, Graaf, Chris de, Tresadern, Gary
Published in Journal of chemical information and modeling (23.11.2020)
Published in Journal of chemical information and modeling (23.11.2020)
Get full text
Journal Article
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology
Liu, Xuhan, Ye, Kai, van Vlijmen, Herman W. T., Emmerich, Michael T. M., IJzerman, Adriaan P., van Westen, Gerard J. P.
Published in Journal of cheminformatics (12.11.2021)
Published in Journal of cheminformatics (12.11.2021)
Get full text
Journal Article
Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study
Keränen, Henrik, Pérez-Benito, Laura, Ciordia, Myriam, Delgado, Francisca, Steinbrecher, Thomas B, Oehlrich, Daniel, van Vlijmen, Herman W. T, Trabanco, Andrés A, Tresadern, Gary
Published in Journal of chemical theory and computation (14.03.2017)
Published in Journal of chemical theory and computation (14.03.2017)
Get full text
Journal Article
Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery
Sabanés Zariquiey, Francesc, Jacoby, Edgar, Vos, Ann, van Vlijmen, Herman W. T, Tresadern, Gary, Harvey, Jeremy
Published in Journal of chemical information and modeling (14.02.2022)
Published in Journal of chemical information and modeling (14.02.2022)
Get full text
Journal Article
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs
Burggraaff, Lindsey, van Veen, Amber, Lam, Chi Chung, van Vlijmen, Herman W. T, IJzerman, Adriaan P, van Westen, Gerard J. P
Published in Journal of chemical information and modeling (26.10.2020)
Published in Journal of chemical information and modeling (26.10.2020)
Get full text
Journal Article
Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling
Tresadern, Gary, Trabanco, Andres A, Pérez-Benito, Laura, Overington, John P, van Vlijmen, Herman W. T, van Westen, Gerard J. P
Published in Journal of chemical information and modeling (26.12.2017)
Published in Journal of chemical information and modeling (26.12.2017)
Get full text
Journal Article
Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors
Burggraaff, Lindsey, Lenselink, Eelke B, Jespers, Willem, van Engelen, Jesper, Bongers, Brandon J, González, Marina Gorostiola, Liu, Rongfang, Hoos, Holger H, van Vlijmen, Herman W. T, IJzerman, Adriaan P, van Westen, Gerard J. P
Published in Journal of chemical information and modeling (28.09.2020)
Published in Journal of chemical information and modeling (28.09.2020)
Get full text
Journal Article
Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation
Lenselink, Eelke B, Louvel, Julien, Forti, Anna F, van Veldhoven, Jacobus P. D, de Vries, Henk, Mulder-Krieger, Thea, McRobb, Fiona M, Negri, Ana, Goose, Joseph, Abel, Robert, van Vlijmen, Herman W. T, Wang, Lingle, Harder, Edward, Sherman, Woody, IJzerman, Adriaan P, Beuming, Thijs
Published in ACS omega (31.08.2016)
Published in ACS omega (31.08.2016)
Get full text
Journal Article
Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data
van Westen, Gerard J P, Hendriks, Alwin, Wegner, Jörg K, Ijzerman, Adriaan P, van Vlijmen, Herman W T, Bender, Andreas
Published in PLoS computational biology (01.02.2013)
Published in PLoS computational biology (01.02.2013)
Get full text
Journal Article
Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development
van Westen, Gerard J P, Wegner, Jörg K, Geluykens, Peggy, Kwanten, Leen, Vereycken, Inge, Peeters, Anik, Ijzerman, Adriaan P, van Vlijmen, Herman W T, Bender, Andreas
Published in PloS one (23.11.2011)
Published in PloS one (23.11.2011)
Get full text
Journal Article
Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A2A Receptor
Lenselink, Eelke B, Beuming, Thijs, Sherman, Woody, van Vlijmen, Herman W. T, IJzerman, Adriaan P
Published in Journal of chemical information and modeling (23.06.2014)
Published in Journal of chemical information and modeling (23.06.2014)
Get full text
Journal Article
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization
van der Horst, Eelke, Peironcely, Julio E, Ijzerman, Adriaan P, Beukers, Margot W, Lane, Jonathan R, van Vlijmen, Herman W T, Emmerich, Michael T M, Okuno, Yasushi, Bender, Andreas
Published in BMC bioinformatics (10.06.2010)
Published in BMC bioinformatics (10.06.2010)
Get full text
Journal Article
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets
van Westen, Gerard JP, Swier, Remco F, Wegner, Jörg K, IJzerman, Adriaan P, van Vlijmen, Herman WT, Bender, Andreas
Published in Journal of cheminformatics (23.09.2013)
Published in Journal of cheminformatics (23.09.2013)
Get full text
Journal Article
Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling
Burggraaff, Lindsey, Oranje, Paul, Gouka, Robin, van der Pijl, Pieter, Geldof, Marian, van Vlijmen, Herman W. T., IJzerman, Adriaan P., van Westen, Gerard J. P.
Published in Journal of cheminformatics (14.02.2019)
Published in Journal of cheminformatics (14.02.2019)
Get full text
Journal Article