Adriaan P. IJzerman

Publication Activity (10 Years)

Years Active: 1988-2023
Publications (10 Years): 18

Top Topics

Reinforcement Learning

Binding Peptides

Virtual Screening

Top Venues

J. Cheminformatics

J. Chem. Inf. Model.

PLoS Comput. Biol.

Briefings Bioinform.

Publications

O. J. M. Béquignon, Brandon J. Bongers, Willem Jespers, Adriaan P. IJzerman, B. van der Water, Gerard J. P. van Westen
Papyrus: a large-scale curated dataset aimed at bioactivity predictions. J. Cheminformatics 15 (1) (2023)
Brandon J. Bongers, Huub J. Sijben, Peter B. R. Hartog, Andrey Tarnovskiy, Adriaan P. IJzerman, Laura H. Heitman, Gerard J. P. van Westen
Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors. J. Chem. Inf. Model. 63 (6) (2023)
Marina Gorostiola González, Remco L. van den Broek, Thomas G. M. Braun, Magdalini Chatzopoulou, Willem Jespers, Adriaan P. IJzerman, Laura H. Heitman, Gerard J. P. van Westen
3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors. J. Cheminformatics 15 (1) (2023)
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)
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)
Willem Jespers, Laura H. Heitman, Adriaan P. IJzerman, Eddy Sotelo, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez-de-Terán
Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations. PLoS Comput. Biol. 17 (11) (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)
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)
Iryna Yevseyeva, Eelke B. Lenselink, Alice de Vries, Adriaan P. IJzerman, André H. Deutz, Michael T. M. Emmerich
Application of portfolio optimization to drug discovery. Inf. Sci. 475 (2019)
Shardul Paricharak, Oscar Méndez-Lucio, Aakash Chavan Ravindranath, Andreas Bender, Adriaan P. IJzerman, Gerard J. P. van Westen
Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. Briefings Bioinform. 19 (2) (2018)
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)
Shardul Paricharak, Adriaan P. IJzerman, Jeremy L. Jenkins, Andreas Bender, Florian Nigsch
Data-Driven Derivation of an "Informer Compound Set" for Improved Selection of Active Compounds in High-Throughput Screening. J. Chem. Inf. Model. 56 (9) (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)
Shardul Paricharak, Isidro Cortes-Ciriano, Adriaan P. IJzerman, Therese E. Malliavin, Andreas Bender
Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules. J. Cheminformatics 7 (2015)
Eelke B. Lenselink, Thijs Beuming, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman
Receptor. J. Chem. Inf. Model. 54 (6) (2014)
Alexios Koutsoukas, Shardul Paricharak, Warren R. J. D. Galloway, David R. Spring, Adriaan P. IJzerman, Robert C. Glen, David Marcus, Andreas Bender
How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space. J. Chem. Inf. Model. 54 (1) (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)
Dan Chen, Anirudh Ranganathan, Adriaan P. IJzerman, Gregg Siegal, Jens Carlsson
Adenosine Receptor. J. Chem. Inf. Model. 53 (10) (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)
Eelke van der Horst, Patricia Marqués-Gallego, Thea Mulder-Krieger, Jacobus van Veldhoven, Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Johannes Brussee, Andreas Bender, Adriaan P. IJzerman
Multi-Objective Evolutionary Design of Adenosine Receptor Ligands. J. Chem. Inf. Model. 52 (7) (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)
Eelke van der Horst, Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Andreas Bender, Adriaan P. IJzerman
Evolutionary design of selective adenosine receptor ligands. J. Cheminformatics 2 (S-1) (2010)
Johannes W. Kruisselbrink, Michael T. M. Emmerich, Thomas Bäck, Andreas Bender, Adriaan P. IJzerman, Eelke van der Horst
Combining Aggregation with Pareto Optimization: A Case Study in Evolutionary Molecular Design. EMO (2009)
Munikumar R. Doddareddy, Gerard J. P. van Westen, Eelke van der Horst, Julio E. Peironcely, Frans Corthals, Adriaan P. IJzerman, Michael Emmerich, Jeremy L. Jenkins, Andreas Bender
Chemogenomics: Looking at biology through the lens of chemistry. Stat. Anal. Data Min. 2 (3) (2009)
Eelke van der Horst, Yasushi Okuno, Andreas Bender, Adriaan P. IJzerman
Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner. J. Chem. Inf. Model. 49 (2) (2009)
Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Adriaan P. IJzerman, Andreas Bender, Thomas Bäck, Eelke van der Horst
Enhancing search space diversity in multi-objective evolutionary drug molecule design using niching. GECCO (2009)
Johannes W. Kruisselbrink, Thomas Bäck, Adriaan P. IJzerman, Eelke van der Horst
Evolutionary algorithms for automated drug design towards target molecule properties. GECCO (2008)
Kai Ye, Gert Vriend, Adriaan P. IJzerman
Tracing evolutionary pressure. Bioinform. 24 (7) (2008)
Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, Elena Marchiori
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. Bioinform. 24 (1) (2008)
Kai Ye, Walter A. Kosters, Adriaan P. IJzerman
An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences. Bioinform. 23 (6) (2007)
Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman
Mining a Chemical Database for Fragment Co-occurrence: Discovery of "Chemical Clichés". J. Chem. Inf. Model. 46 (2) (2006)
Elena V. Samsonova, Joost N. Kok, Adriaan P. IJzerman
TreeSOM: Cluster analysis in the self-organizing map. Neural Networks 19 (6-7) (2006)
Jeroen Kazius, Siegfried Nijssen, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman
Substructure Mining Using Elaborate Chemical Representation. J. Chem. Inf. Model. 46 (2) (2006)
Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman
The Molecule Evoluator. An Interactive Evolutionary Algorithm for the Design of Drug-Like Molecules. J. Chem. Inf. Model. 46 (2) (2006)
Elena V. Samsonova, Thomas Bäck, Joost N. Kok, Adriaan P. IJzerman
Reliable Hierarchical Clustering with the Self-organizing Map. IDA (2005)
Eric-Wubbo Lameijer, Adriaan P. IJzerman, Joost N. Kok
Using data mining to improve mutation in a tool for molecular evolution. Congress on Evolutionary Computation (2005)
Eric-Wubbo Lameijer, Adriaan P. IJzerman, Joost N. Kok
The molecule evoluator: an interactive evolutionary algorithm for designing drug molecules. GECCO (2005)
Eric-Wubbo Lameijer, Thomas Bäck, Joost N. Kok, Adriaan P. IJzerman
Evolutionary Algorithms in Drug Design. Nat. Comput. 4 (3) (2005)
Elena V. Samsonova, Thomas Bäck, Margot W. Beukers, Adriaan P. IJzerman, Joost N. Kok
Combining and Comparing Cluster Methods in a Receptor Database. IDA (2003)
Eleonora M. van der Wenden, Sarah L. Price, Robert P. Apaya, Adriaan P. IJzerman, Willem Soudijn
receptor ligands - A test case for Distributed Multipole Analysis in medicinal chemistry. J. Comput. Aided Mol. Des. 9 (1) (1995)
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)