Adriaan P. IJzerman

50 papers A 3B 3C 1Journal 42

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors. J. Cheminformatics 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
2023	J	`jnl`	DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning. J. Cheminformatics Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2023	J	`jnl`	Papyrus: a large-scale curated dataset aimed at bioactivity predictions. J. Cheminformatics Olivier J. M. Béquignon, Brandon J. Bongers, Willem Jespers, Adriaan P. IJzerman, B. van der Water, Gerard J. P. van Westen
2023	J	`jnl`	Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors. J. Chem. Inf. Model. Brandon J. Bongers, Huub J. Sijben, Peter B. R. Hartog, Andrey Tarnovskiy, Adriaan P. IJzerman, Laura H. Heitman, Gerard J. P. van Westen
2021	—	`ch.`	Computational Approaches for De Novo Drug Design: Past, Present, and Future. Artificial Neural Networks, 3rd Edition Xuhan Liu, Adriaan P. IJzerman, Gerard J. P. van Westen
2021	J	`jnl`	Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations. PLoS Comput. Biol. Willem Jespers, Laura H. Heitman, Adriaan P. IJzerman, Eddy Sotelo, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez-de-Terán
2021	J	`jnl`	DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology. J. Cheminformatics Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Adriaan P. IJzerman, Gerard J. P. van Westen
2020	J	`jnl`	Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. J. Chem. Inf. Model. Lindsey Burggraaff, Amber van Veen, Chi Chung Lam, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2020	J	`jnl`	Quantitative prediction of selectivity between the A J. Cheminformatics Lindsey Burggraaff, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2020	J	`jnl`	Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. J. Chem. Inf. Model. 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
2019	J	`jnl`	Advances and Challenges in Computational Target Prediction. J. Chem. Inf. Model. Dominique Sydow, Lindsey Burggraaff, Angelika Szengel, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen, Andrea Volkamer
2019	J	`jnl`	An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor. J. Cheminformatics Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2019	J	`jnl`	Application of portfolio optimization to drug discovery. Inf. Sci. Iryna Yevseyeva, Eelke B. Lenselink, Alice de Vries, Adriaan P. IJzerman, André H. Deutz, Michael T. M. Emmerich
2019	J	`jnl`	Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling. J. Cheminformatics 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
2018	J	`jnl`	Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. Briefings Bioinform. Shardul Paricharak, Oscar Méndez-Lucio, Aakash Chavan Ravindranath, Andreas Bender, Adriaan P. IJzerman, Gerard J. P. van Westen
2017	J	`jnl`	Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set. J. Cheminformatics 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
2016	J	`jnl`	Data-Driven Derivation of an "Informer Compound Set" for Improved Selection of Active Compounds in High-Throughput Screening. J. Chem. Inf. Model. Shardul Paricharak, Adriaan P. IJzerman, Jeremy L. Jenkins, Andreas Bender, Florian Nigsch
2016	J	`jnl`	In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor. J. Comput. Aided Mol. Des. Eelke B. Lenselink, Thijs Beuming, Corine van Veen, Arnault Massink, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman
2016	J	`jnl`	Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening. J. Chem. Inf. Model. Eelke B. Lenselink, Willem Jespers, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2015	J	`jnl`	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 Shardul Paricharak, Isidro Cortes-Ciriano, Adriaan P. IJzerman, Therese E. Malliavin, Andreas Bender
2014	J	`jnl`	How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space. J. Chem. Inf. Model. Alexios Koutsoukas, Shardul Paricharak, Warren R. J. D. Galloway, David R. Spring, Adriaan P. IJzerman, Robert C. Glen, David Marcus, Andreas Bender
2014	J	`jnl`	Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A J. Chem. Inf. Model. Eelke B. Lenselink, Thijs Beuming, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman
2013	J	`jnl`	Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. J. Cheminformatics Gerard J. P. van Westen, Remco F. Swier, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
2013	J	`jnl`	Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. J. Cheminformatics 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
2013	J	`jnl`	Complementarity between in Silico and Biophysical Screening Approaches in Fragment-Based Lead Discovery against the A J. Chem. Inf. Model. Dan Chen, Anirudh Ranganathan, Adriaan P. IJzerman, Gregg Siegal, Jens Carlsson
2013	J	`jnl`	Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data. PLoS Comput. Biol. Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
2012	J	`jnl`	Multi-Objective Evolutionary Design of Adenosine Receptor Ligands. J. Chem. Inf. Model. 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
2010	J	`jnl`	A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. BMC Bioinform. 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
2010	J	`jnl`	Evolutionary design of selective adenosine receptor ligands. J. Cheminformatics Eelke van der Horst, Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Andreas Bender, Adriaan P. IJzerman
2010	J	`jnl`	Molecular bioactivity extrapolation to novel targets by support vector machines. J. Cheminformatics Gerard J. P. van Westen, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
2009	J	`jnl`	Chemogenomics: Looking at biology through the lens of chemistry. Stat. Anal. Data Min. 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
2009	C	`conf`	Combining Aggregation with Pareto Optimization: A Case Study in Evolutionary Molecular Design. EMO Johannes W. Kruisselbrink, Michael T. M. Emmerich, Thomas Bäck, Andreas Bender, Adriaan P. IJzerman, Eelke van der Horst
2009	A	`conf`	Enhancing search space diversity in multi-objective evolutionary drug molecule design using niching. GECCO Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Adriaan P. IJzerman, Andreas Bender, Thomas Bäck, Eelke van der Horst
2009	J	`jnl`	Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner. J. Chem. Inf. Model. Eelke van der Horst, Yasushi Okuno, Andreas Bender, Adriaan P. IJzerman
2008	A	`conf`	Evolutionary algorithms for automated drug design towards target molecule properties. GECCO Johannes W. Kruisselbrink, Thomas Bäck, Adriaan P. IJzerman, Eelke van der Horst
2008	J	`jnl`	Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. Bioinform. Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, Elena Marchiori
2008	J	`jnl`	Tracing evolutionary pressure. Bioinform. Kai Ye, Gert Vriend, Adriaan P. IJzerman
2007	J	`jnl`	An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences. Bioinform. Kai Ye, Walter A. Kosters, Adriaan P. IJzerman
2006	J	`jnl`	Mining a Chemical Database for Fragment Co-occurrence: Discovery of "Chemical Clichés". J. Chem. Inf. Model. Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman
2006	J	`jnl`	Substructure Mining Using Elaborate Chemical Representation. J. Chem. Inf. Model. Jeroen Kazius, Siegfried Nijssen, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman
2006	J	`jnl`	The Molecule Evoluator. An Interactive Evolutionary Algorithm for the Design of Drug-Like Molecules. J. Chem. Inf. Model. Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman
2006	J	`jnl`	TreeSOM: Cluster analysis in the self-organizing map. Neural Networks Elena V. Samsonova, Joost N. Kok, Adriaan P. IJzerman
2005	J	`jnl`	Evolutionary Algorithms in Drug Design. Nat. Comput. Eric-Wubbo Lameijer, Thomas Bäck, Joost N. Kok, Adriaan P. IJzerman
2005	B	`conf`	Reliable Hierarchical Clustering with the Self-organizing Map. IDA Elena V. Samsonova, Thomas Bäck, Joost N. Kok, Adriaan P. IJzerman
2005	A	`conf`	The molecule evoluator: an interactive evolutionary algorithm for designing drug molecules. GECCO Eric-Wubbo Lameijer, Adriaan P. IJzerman, Joost N. Kok
2005	B	`conf`	Using data mining to improve mutation in a tool for molecular evolution. Congress on Evolutionary Computation Eric-Wubbo Lameijer, Adriaan P. IJzerman, Joost N. Kok
2003	B	`conf`	Combining and Comparing Cluster Methods in a Receptor Database. IDA Elena V. Samsonova, Thomas Bäck, Margot W. Beukers, Adriaan P. IJzerman, Joost N. Kok
1995	J	`jnl`	Relative binding orientations of adenosine A J. Comput. Aided Mol. Des. Eleonora M. van der Wenden, Sarah L. Price, Robert P. Apaya, Adriaan P. IJzerman, Willem Soudijn
1989	J	`jnl`	Molecular modeling of a putative antagonist binding site on helix III of the β-adrenoceptor. J. Comput. Aided Mol. Des. Herman W. T. van Vlijmen, Adriaan P. IJzerman
1988	J	`jnl`	A molecular graphics study exploring a putative ligand binding site of the J. Comput. Aided Mol. Des. Adriaan P. IJzerman, Herman W. T. van Vlijmen