Publications

Please click for pre-prints when not OA. 


 
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
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