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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)
Coauthor Index
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