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Adriaan P. IJzerman
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2020 – today
- 2023
- [j42]Olivier 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): 3 (2023) - [j41]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) - [j40]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): 74 (2023) - [j39]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): 1745-1755 (2023) - 2021
- [j38]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) - [j37]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) - [p1]Xuhan Liu
, Adriaan P. IJzerman
, Gerard J. P. van Westen
:
Computational Approaches for De Novo Drug Design: Past, Present, and Future. Artificial Neural Networks, 3rd Edition 2021: 139-165 - 2020
- [j36]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) - [j35]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) - [j34]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)
2010 – 2019
- 2019
- [j33]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: 29-43 (2019) - [j32]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) - [j31]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) - [j30]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) - 2018
- [j29]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): 277-285 (2018) - 2017
- [j28]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) - 2016
- [j27]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) - [j26]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): 1622-1630 (2016) - [j25]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
- [j24]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: 15 (2015) - 2014
- [j23]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): 230-242 (2014) - [j22]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
- [j21]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) - [j20]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) - [j19]Dan Chen, Anirudh Ranganathan, Adriaan P. IJzerman
, Gregg Siegal
, Jens Carlsson
:
Complementarity between in Silico and Biophysical Screening Approaches in Fragment-Based Lead Discovery against the A2A Adenosine Receptor. J. Chem. Inf. Model. 53(10): 2701-2714 (2013) - [j18]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
- [j17]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): 1713-1721 (2012) - 2010
- [j16]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) - [j15]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) - [j14]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): 48 (2010)
2000 – 2009
- 2009
- [j13]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): 348-360 (2009) - [j12]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): 149-160 (2009) - [c7]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: 453-467 - [c6]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: 217-224 - 2008
- [j11]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): 18-25 (2008) - [j10]Kai Ye
, Gert Vriend, Adriaan P. IJzerman
:
Tracing evolutionary pressure. Bioinform. 24(7): 908-915 (2008) - [c5]Johannes W. Kruisselbrink, Thomas Bäck, Adriaan P. IJzerman, Eelke van der Horst:
Evolutionary algorithms for automated drug design towards target molecule properties. GECCO 2008: 1555-1562 - 2007
- [j9]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): 687-693 (2007) - 2006
- [j8]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): 545-552 (2006) - [j7]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): 553-562 (2006) - [j6]Jeroen Kazius, Siegfried Nijssen
, Joost N. Kok, Thomas Bäck
, Adriaan P. IJzerman
:
Substructure Mining Using Elaborate Chemical Representation. J. Chem. Inf. Model. 46(2): 597-605 (2006) - [j5]Elena V. Samsonova, Joost N. Kok, Adriaan P. IJzerman
:
TreeSOM: Cluster analysis in the self-organizing map. Neural Networks 19(6-7): 935-949 (2006) - 2005
- [j4]Eric-Wubbo Lameijer, Thomas Bäck
, Joost N. Kok, Adriaan P. IJzerman:
Evolutionary Algorithms in Drug Design. Nat. Comput. 4(3): 177-243 (2005) - [c4]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: 314-321 - [c3]Eric-Wubbo Lameijer, Adriaan P. IJzerman, Joost N. Kok:
The molecule evoluator: an interactive evolutionary algorithm for designing drug molecules. GECCO 2005: 1969-1976 - [c2]Elena V. Samsonova, Thomas Bäck
, Joost N. Kok, Adriaan P. IJzerman:
Reliable Hierarchical Clustering with the Self-organizing Map. IDA 2005: 385-396 - 2003
- [c1]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: 341-351
1990 – 1999
- 1995
- [j3]Eleonora M. van der Wenden, Sarah L. Price, Robert P. Apaya, Adriaan P. IJzerman
, Willem Soudijn:
Relative binding orientations of adenosine A1 receptor ligands - A test case for Distributed Multipole Analysis in medicinal chemistry. J. Comput. Aided Mol. Des. 9(1): 44-54 (1995)
1980 – 1989
- 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)
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