Publications

Please click for pre-prints when not OA.

53 An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning:
a case for the adenosine A2A receptor

      Journal of Cheminformatics (2019), 11, 35, https://doi.org/10.1007/s12471-019-1282-x
           Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, and Gerard J. P. van Westen

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0355-6

52 Body mass index related electrocardiographic findings in healthy young individuals with a normal body mass index

Netherlands Heart Journal (2019), in press, doi:https://doi.org/10.1007/s12471-019-1282-x
G. J. Hassing, H. E. C. van der Wall, G. J. P. van Westen, M. J. B. Kemme, A. Adiyaman, A. Elvan, J. Burggraaf, P. Gal

https://link.springer.com/article/10.1007%2Fs12471-019-1282-x

51 In vitro 3d phenotypic drug screen identifies celastrol as an effective in vivo inhibitor of polycystic kidney disease

       Journal of Molecular Cell Biology (2019), in press https://doi.org/10.1093/jmcb/mjz029
       Tijmen H. Booij, Wouter N. Leonhard, Hester Bange, Kuan Yan, Michiel Fokkelman, Anna J. Plugge, Kimberley A.M/ Veraar, Johannes G. Dauwerse,
       Gerard J.P. van Westen, Bob van de Water, Leo S. Price, and Dorien J. M. Peters

https://academic.oup.com/jmcb/advance-article/doi/10.1093/jmcb/mjz029/5486613

50 Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling

       Journal of Chemical Information and Modeling (2019), 11 (15) https://doi.org/10.1186/s13321-019-0337-8
       Lindsey Burggraaff, Paul Oranje, Robin Gouka, Pieter van der Pijl, Marian Geldof, Herman W. T. van Vlijmen, Adriaan P. IJzerman,
       and Gerard J.P. van Westen

49 Advances and Challenges in Computational Target Prediction

       Journal of Chemical Information and Modeling (2019), In press, https://doi.org/10.1021/acs.jcim.8b00832
       Dominique Sydow , Lindsey Burggraaff , Angelika Szengel, Herman W. T. van Vlijmen , Adriaan P. IJzerman ,
       Gerard J. P. van Westen , and Andrea Volkamer

48 Number of ECG Replicates and QT Correction Formula Influences the Estimated QT Prolonging Effect of a Drug

Journal of Cardiovascular Pharmacology (2019), 73 (4), 257–264 https://doi.org/10.1097/FJC.0000000000000657
Hein Evert Christiaan van der Wall, Pim Gal, Michiel J. B. Kemme, Gerard.J.P. van Westen, and Koos Burggraaf

47 Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors

        Bioorganic & Medicinal Chemistry (2019), 27 (5), 692-699, https://doi.org/10.1016/j.bmc.2019.01.006
       Sebastian H. Grimm, Berend Gagestein, Jordi F. Keijzer, Nora Liu, Ruud H. Wijdeven, Eelke B. Lenselink, Adriaan W. Tuind, Adrianus M.C.H.van den
       Nieuwendijk, Gerard J.P.van Westen, Constant A.A.van Boeckel, Herman S. Overkleeft, Jacques Neefjes, Mario van der Stelt

46 Activity-Based Protein Profiling Identifies α-Ketoamides as Inhibitors for Phospholipase A2 Group XVI

        ACS Chemical Biology (2019), In press, https://doi.org/10.1021/acschembio.8b00969
       Juan Zhou, Elliot D. Mock, Andrea Martella, Vasudev Kantae, Xinyu Di, Lindsey Burggraaff, Marc P. Baggelaar, Karol Al-Ayed, Alexander Bakker, Bogdan I.
       Florea, Sebastian H. Grimm, Hans den Dulk, Chun T. Li, Laura Mulder, Herman S. Overkleeft, Thomas Hankemeier, Gerard J. P. van Westen, and
       Mario van der Stelt

45 Novel technologies for metabolomics: More for less

TrAC (2018), In press, https://doi.org/10.1016/j.trac.2018.11.021
Paul Miggiels, Bert Wouters, Gerard J.P.van Westen, Anne-Charlotte Dubbelman ,Thomas Hankemeier

44 Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome–Inhibitor Interaction Landscapes

        JCIM (2018), In press, https://doi.org/10.1021/acs.jcim.8b00640
       Antonius P. A. Janssen, Sebastian H. Grimm, Ruud H. M. Wijdeven, Eelke B. Lenselink, Jacques Neefjes, Constant A. A. van Boeckel,
       Gerard J. P. van Westen, and Mario van der Stelt

43 Linking drug target and pathway activation for effective therapy using multi-task learning

Scientific Reports (2018), 8322, https://doi.org/10.1038/s41598-018-25947-y
Mi Yang, Jaak Simm, Chi Chung Lam, Pooya Zakeri, Gerard J. P. van Westen, Yves Moreau and Julio Saez-Rodriguez

42 Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling

J. Chem. Inf. Model. (2018), In Press, doi: https://doi.org/10.1021/acs.jcim.7b00338
Gary Tresadern, Andres A. Trabanco , Laura Pérez-Benito, John P. Overington, Herman W. T. van Vlijmen, and Gerard J. P. van Westen

41 Target and Tissue Selectivity Prediction by Integrated Mechanistic Pharmacokinetic-Target Binding and Quantitative Structure
Activity Modeling

The AAPS Journal (2018), In Press, doi: https://doi.org/10.1208/s12248-017-0172-7
Anna H. C. Vlot, Wilhelmus E. A. de Witte, Meindert Danhof, Piet H. van der Graaf, Gerard J. P. van Westen, Elizabeth C. M. de Lange

40 Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms

        TiPS (2018), In Press, doi: https://dx.doi.org/10.1016/j.tips.2017.11.001
       Willem Jespers, Anke C. Schiedel, Laura H. Heitman, Robert M. Cooke, Lisa Kleene, Gerard J. P. van Westen, David E. Gloriam, Christa E. Müller,
       Eddy Sotelo and Hugo Gutiérrez-de-Terán

39 Reduced hepatitis B and D viral entry using clinically applied drugs as novel inhibitors of the bile acid transporter NTCP

Nature Scientific Reports (2017), 7, Article number: 15307, doi: https://10.1038/s41598-017-15338-0
Joanne M. Donkers, Benno Zehnder, Gerard J. P. van Westen, Mark J. Kwakkenbos, Adriaan P. IJzerman, Ronald P. J. Oude Elferink, Ulrich Beuers,
Stephan Urban and Stan F. J. van de Graaf

38 Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set

J Cheminf (2017), 9:45 doi: https://10.1186/s13321-017-0232-0
Eelke B. Lenselink, Niels ten Dijke, Brandon Bongers, George Papadatos, Herman W. T. van Vlijmen, Wojtek Kowalczyk, Adriaan P. IJzerman,
and Gerard J. P. van Westen

37 High-Throughput Phenotypic Screening of Kinase Inhibitors to Identify Drug Targets for Polycystic Kidney Disease

SLAS Discov. (2017), 22 doi: https://10.1177/2472555217716056
Tijmen H. Booij, Hester Bange, Wouter N. Leonhard, Kuan Yan, Michiel Fokkelman, Steven J. Kunnen, Johannes G. Dauwerse, Yu Qin, Bob van de Water, Gerard J. P. van Westen, Dorien J. M. Peters, and Leo S. Price

36 Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening

Brief Bioinform (2016), bbw105, doi: https://doi.org/10.1093/bib/bbw105
Shardul Paricharak, Oscar Méndez-Lucio, Aakash Chavan Ravindranath, Andreas Bender, Adriaan P. IJzerman, and Gerard J. P. van Westen

35 Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening

JCIM (2016), 56, 10, doi: 10.1021/acs.jcim.6b00314
Eelke B. Lenselink, Willem Jespers, Herman W. T. van Vlijmen, Adriaan P. IJzerman, and Gerard J. P. van Westen

34 Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound–Kinase Activities: A Way toward Selective Promiscuity by Design?

JCIM (2016), 56, 9, doi: 10.1021/acs.jcim.6b00122
Serge Christmann-Franck, Gerard J. P. van Westen, George Papadatos, Fanny Beltran Escudie, Alexander Roberts, John P. Overington, and Daniel Domine

33 Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel

Bioinformatics (2016), 32, 85-95. doi: 10.1093/bioinformatics/btv529., pre-print version available here
Isidro Cortés-Ciriano, Gerard J.P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, and Thérèse E. Malliavin

32 Chemically Aware Model Builder (camb): An R package for property and bioactivity modelling of small molecules

Journal of Cheminformatics (2015), 7, 45, doi: 10.1186/s13321-015-0086-2
Daniel S. Murrell, Isidro Cortes-Ciriano, Gerard J.P. van Westen, Ian Stott, Andreas Bender, Therese E. Malliavin, and Robert C. Glen

31 A large-scale crop protection bioassay data set

        Scientific Data (2015), 2, 150032  doi: 10.1038/sdata.2015.32
        Anna Gaulton, Namrata Kale, Gerard J.P. van Westen, Louisa J. Bellis, A. Patrícia Bento, Mark Davies, Anne Hersey, George Papadatos, Mark
       Forster, Philip Wege, and John P. Overington

30 Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation

        PLoS ONE (2015), 10(3) , e0121492 doi: 10.1371/journal.pone.0121492
        Grace Mugumbate, Katherine A Abrahams, Jonathan AG Cox, George Papadatos, Gerard JP van Westen, Joel Lelievre, Szymon T Calus, Nick Loman, Lluis
       Ballell, David Barros, John P Overington, Gurdyal S Besra

29 Optogenetic activation of intracellular adenosine A2A receptor signaling in the hippocampus is sufficient to trigger CREB
phosphorylation and impair memory

        Mol. Psychiatry (2015) In press doi:10.1038/mp.2014.182
        P Li, D Rial, P M Canas, J-H Yoo, W Li, X Zhou, Y Wang, Gerard JP van Westen, M-P Payen, E Augusto, N Gonçalves, A R Tomé, Z Li, Z Wu, X Hou, Y
       Zhou, Adriaan P IJzerman, E S Boyden, R A Cunha, J Qu and J-F Chen

28 A community computational challenge to predict the activity of pairs of compounds

        Nature Biotech (2014) 32 doi:10.1038/nbt.3052
        Mukesh Bansal, Jichen Yang, Charles Karan, Michael P Menden, James C Costello, Hao Tang, Guanghua Xiao,Yajuan Li,Jeffrey Allen,Rui Zhong,Beibei
       Chen,Minsoo Kim,Tao Wang,Laura M Heiser,Ronald Realubit,Michela Mattioli,Mariano J Alvarez,Yao Shen, Gerard JP van Westen, NCI-DREAM
       Community,Daniel Gallahan,Dinah Singer,Julio Saez-Rodriguez,Yang Xie,Gustavo Stolovitzky, and Andrea Califano

27 Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling

J Cheminf (2015) 7 (1) doi:10.1186/s13321-014-0049-z
Isidro Cortes-Ciriano, Daniel S Murrell, Gerard JP van Westen, Andreas Bender, and Thérèse E Malliavin

26 Polypharmacology Modelling Using Proteochemometrics (PCM): Recent Methodological Developments, Applications to Target Families, and Future Prospects

        MedChemComm (2014) In press doi:10.1039/C4MD00216D
        Isidro Cortes-Ciriano, Qurrat ul Ain, Vigneshwari Subramanian, Bart Lenselink, Oscar Mendez-Lucio, Adriaan P. IJzerman, Gerd Wohlfahrt, Peteris Prusis,
  Thérèse E Malliavin, Gerard J.P. van Westen, and Andreas Bender

25 MyChEMBL: A Virtual Platform for Distributing Cheminformatics Tools and Open Data

Challenges (2014) 5 334-337 doi:10.3390/challe5020334
Mark Davies, Michał Nowotka, George Papadatos, Francis Atkinson, Gerard J. P. van Westen, Nathan Dedman, Rodrigo Ochoa, and John P. Overington

24 Modelling ligand selectivity of Serine Proteases using integrative Proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features

Integrative Biology (2014) In Press doi: 10.1039/C4IB00175C
Qurrat U Ain, Oscar Méndez-Lucio, Isidro Cortés Ciriano, Thérèse Malliavin, Gerard J.P. van Westen, and Andreas Bender

23 Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges

Structure (2014) 22 (8) 1120-1139 doi:10.1016/j.str.2014.06.012
Irina Kufareva, Vsevolod Katritch, Participants of GPCR Dock2013 (Gerard J.P. van Westen), Raymond C. Stevens, Ruben Abagyan

22 Domains for activation and inactivation in G protein-coupled receptors–a mutational analysis of constitutive activity of the adenosine A2B receptor

Biochemical Pharmacology (2014) In Press, doi:10.1016/j.bcp.2014.08.022
Miriam C. Peeters, Qilan Li, Rachel Elands, Gerard J.P. van Westen, Eelke B. Lenselink, Christa E. Müller, Adriaan P. IJzerman

21 Random Forest ensembles for detection and prediction of Alzheimer's Disease with a good between-cohort robustness

Neuroimage: Clinical (2014) 6 115–125 doi: 10.1016/j.nicl.2014.08.023
Alexander V. Lebedev, Eric Westman, Gerard J.P. Van Westen, Milica G. Kramberger, Arvid Lundervold, Dag Aarsland, Hillka Soininen, Iwona Kłoszewska, Patrizia Mecocci, Magda Tsolaki, Bruno Vellas, Simon Lovestone, Andy Simmons

20 A document classifier for medicinal chemistry publications trained on the ChEMBL corpus

Journal of Cheminformatics (2014) 6:40 doi:10.1186/s13321-014-0040-8
George Papadatos, Gerard J.P. van Westen, Samuel Croset, Rita Santos, Simone Trubian and John P. Overington

19 Proteochemometric modeling in a Bayesian framework

Journal of Cheminformatics (2014) 6:35 doi:10.1186/1758-2946-6-35
Isidro Cortes-Ciriano, Gerard J.P. van Westen, Eelke Bart Lenselink, Daniel S. Murrell, Andreas Bender and Thérèse Malliavin

18 A community effort to assess and improve drug sensitivity prediction algorithms

Nature Biotechnology (2014) in press doi:10.1038/nbt.2877
James C Costello, Laura M Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P Menden, Gerard J. P. van Westen, Julio Saez-Rodriguez, Samuel Kaski, Joe W Gray, Gustavo Stolovitzky, et al

17 Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling

Journal of Chemical Biology (2014) in press doi:10.1007/s12154-014-0112-2
Gerard J. P. van Westen, Andreas Bender, John P Overington

16 Chemical, Target, and Bioactive Properties of Allosteric Modulation

PLoS Computational Biology (2014) 10 (4) e1003559 doi:10.1371/journal.pcbi.1003559
Gerard J. P. van Westen, Anna Gaulton ,John P Overington

15 Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets

Journal of Cheminformatics (2013) 5 : 42 doi:10.1186/1758-2946-5-42
Gerard J. P. van Westen, Remco F Swier, Isidro Cortes-Ciriano, Jörg K Wegner,John P Overington,Adriaan P IJzerman, Herman WT van Vlijmen and Andreas Bender

14   Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets
       Journal of Cheminformatics (2013) 5 : 41 doi:10.1186/1758-2946-5-41
       Gerard J. P. van Westen, Remco F Swier, Jörg K Wegner, Adriaan P IJzerman, Herman WT van Vlijmen and Andreas Bender

13   Structure-based Identification of OATP1B1/3 Inhibitors
       Molecular Pharmacology (2013) 83 , 1257-1267 doi:10.1124/mol.112.084152
       Tom De Bruyn, Gerard J. P. van Westen, Adriaan P. IJzerman, Bruno Stieger, Peter de Witte, Patrick F. Augustijns, and Pieter P. Annaert

12   A ligand's-eye view of protein similarity
       Nature Methods (2013) 10 , 116–117 doi:10.1038/nmeth.2339
       Gerard J. P. van Westen and John P. Overington

11 Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram
Data
PLoS Computational Biology (2013) 9(2): e1002899 Doi: 10.1371/journal.pcbi.1002899
Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W.T. van Vlijmen, and Andreas Bender

10   Identifying Novel Adenosine Receptor Ligands by Simultaneous Proteochemometric Modeling of Rat and Human Bioactivity
Data
       Journal of Medicinal Chemistry (2012) 55 (16), 7010-7020 Doi: 10.1021/jm3003069
       Gerard J. P. van Westen, Olaf O. van den Hoven, Rianne van der Pijl, Thea Mulder-Krieger, Henk de Vries, Jörg K. Wegner, Adriaan P. IJzerman,
       Herman W.T. Van Vlijmen, and Andreas Bender

9   A Novel Non-ribose Agonist, LUF5834, Engages Distinct Residues from that of Adenosine-like Ligands to Activate the Adenosine
      A2A Receptor
       Molecular Pharmacology(2012) 81 (3), 475-487 Doi: 10.1124/mol.111.075937
       Robert Lane, Carmen Klein Herenbrink, Gerard J. P. van Westen, Jelle A Spoorendonk, Carsten Hoffmann, Adriaan P. IJzerman

8   Which Compound to Select in Lead Optimization? Prospectively Validated Proteochemometric Models Guide Preclinical
  Development
         Pre-print version available on this site, please see Publishers site above.
       PLoS ONE (2011) 6 (11), e27518
        Gerard J. P. van Westen, Jörg K. Wegner, Peggy Geluykens, Leen Kwanten, Inge Vereycken, Anik Peeters,
       Adriaan P. IJzerman, Herman W.T. van Vlijmen and Andreas Bender

7   Three “hotspots” important for adenosine A2B receptor activation: a mutational analysis of transmembrane domains 4 and 5 and the second extracellular loop
        Purinergic Signalling(2011) 8 (1), 23-38 DOI: 10.1007/s11302-011-9251-x
        Miriam C. Peeters, Qilan Li,Gerard J. P. van Westen, Adriaan P. IJzerman

6   GPCR structure and activation: an essential role for the first extracellular loop in activating the adenosine A2B receptor
        FASEB Journal (2011) 25 (2),632-643 PMID: 21030693
        Miriam C. Peeters,Gerard J. P. van Westen, Dong Guo, Lisanne. E. Wisse, Christa. E. Müller, Margot W. Beukers, Adriaan P. IJzerman

5   The importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation
        Trends in Pharmacological Sciences (2011) 32 (1), 35-42 PMID: 21075459
        Miriam C. Peeters, Gerard J. P. van Westen, Qilan Li, Adriaan P. IJzerman

4   Proteochemometric Modeling as a Tool to Design Selective Compounds and for Extrapolating to Novel Targets
        Medicinal Chemistry Communications (2011) 2, 16-30
        Gerard J. P. van Westen, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender

3   ChemogenomicsApproaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space
      Pre-print version available on this site, please see Publishers site above.
       Current Topics in Medicinal Chemistry (2011) 11 (15), 1964-1977,

PMID: 21470175

Eelke van der Horst, Julio E. Peironcely, Gerard J. P. van Westen, Olaf O. van den Hoven, Warren R. J. D. Galloway, David R. Spring, Joerg K. Wegner,
Herman W. T. van Vlijmen, Ad P. IJzerman, John P. Overington and Andreas Bender

2   Mining protein dynamics from sets of crystal structures using "consensus structures"
        Pre-print version available on this site, please see Publishers site above.
       Protein Science (2010) 19 (4), 742-752, PMID: 20120021
        Gerard J. P. van Westen, Jörg K. Wegner, Andreas Bender, Adriaan P. IJzerman, Herman W. T. van Vlijmen

1   Chemogenomics: Looking at biology through the lens of chemistry
       Statistical Analysis and Data Mining (2009) 2 (3), 149 - 160
       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