Gerard JP van Westen, PhD

Skills

Cheminformatics, statistical modeling (R, Python, Random forest, Naïve bayesian), Big data analysis, visualization & dimensionality reduction (MDS, PCA, etc), structure based modeling (MOE, ICM, Schrodinger, CHARMM, NAMD, etc), workflow tools (Knime, Pipeline Pilot), SQL (MySQL, Oracle, administration), Linux (CentOS, Ubuntu, administration), Cluster calculations (LSF, MPI, R in a cluster environment), CUDA (PyCuda, Cudatrees)

Scientific Publications

36 Peer reviewed works in international journals (h Index 19), multiple talks and numerous poster presentations at scientific conferences. See http://scholar.google.co.uk/citations?user=H7farnwAAAAJ&hl=en&oi=ao

Scientific and personal interests

Predictive polypharmacology, cheminformatics, text mining, text classification, interdisciplinary research, big data, visualization

Computer geek (likes tinkering with hardware and networks), ZFS, open fire cooking, likes driving / road tripping

Current Position

Assitant Professor (Tenure Track) 07-2016 - Present  

• Computational Chemical Biology (Drug & Target Discovery Cluster)

Guest Scientist Leiden University Medical Center 07-2017 - Present  

Previous Positions

Senior Postdoc 05-2015 - 07-2016  

• Computational Chemical Biology (Drug & Target Discovery Cluster)

Senior Postdoc ChEMBL group 11-2013 - 05-2015  

• EMBL Interdisciplinary POstDoc (EIPOD) fellowship

Guest Scientist Leiden University (LACDR) 09-2014 - 04-2015  

Guest Lecturer University of Strathclyde (Glasgow) 12-2013 - 12-2014  

Guest Scientist University of Cambridge 08-2014  

Postdoctoral fellow ChEMBL group 05-2012 - 11-2013  

• EMBL Interdisciplinary POstDoc (EIPOD) fellowship

Grants and Awards

Grant: NWO Veni Personal grant (2015)  

'Discoverer of the year 2013' (Faculty of Science, Leiden University) (2014)  

Grant: EMBL Interdisciplinary POstDoc (EIPOD) / Marie Curie (COFUND) (2011)  

Best presentation in the Pharmacochemistry session at (FIGON Days) (2011)  

Silver poster prize awarded by the KNCV (FIGON Days) (2010)  

Bronze prize in the national Ph.D. student competition (FIGON Days) (2010)  

LACDR Ph.D- student competition for best oral presentation (2010)  

Grant: Personal Ph.D. grant sponsored by Janssen Pharmaceutica (2007)  

Consultancy work

CULGI (chemical modeling company, Leiden, Netherlands)

Stage Pharma (biotech startup, Utrecht, Netherlands)

• Generation of polypharmacological predictive models (aminergic GPCRs)

Johnson & Johnson Pharmaceuticals (Beerse, Belgium)

• Johnson & Johnson Pharmaceuticals (Beerse, Belgium)
• Interpreting HIV-1 Reverse Transcriptase crystal structures

Education

Ph.D. in Proteochemometrics (polypharmacology modeling) 11-2007 – 01-2013     Leiden / Amsterdam Center for Drug Research (Leiden University, The Netherlands)

• Predictive computational models using ligand and protein similarity simultaneously (Proteochemometrics, Ph.D. position was funded by Tibotec BVBA (Johnson and Johnson Pharmaceuticals)

M.Sc. Bio-Pharmaceutical Sciences 09-2001 – 09-2007     Leiden University (Leiden, The Netherlands) with the following research projects:

• Characterizing the inhibition of P-Selectin by GA-GWVDV (36 weeks, molecular biology; department of Bio-Pharmaceutics of the LACDR)
• Characterizing HIV-1 Reverse Transcriptase Non-Nucleoside Reverse Transcriptase Inhibitor Resistance (24 weeks, chem-informatics, department of Chem-informatics and Modeling of Tibotec / Janssen Belgium)

Student Supervision and Teaching

Cheminformatics in Minor ‘Modern Drug Discovery’ (Leiden University)

Thesis examiner at the University of Cambridge (Proteochemometrics)

Designed practical course “Computational Drug Design”, 10-day course on the fundamentals of computational drug design. (given twice to 20 students)

Supervision of 1 Postdoc, 8 M.Sc. students, and 11 B.Sc. students

Reviewing Activities

Ad hoc referee for the following peer reviewed journals: ACS Medicinal Chemistry Letters. Bioinformatics, Journal of Structural Biology, Journal of Medicinal Chemistry, Journal of Chemical Information & Modeling, Journal of Cheminformatics, Molecular Informatics, Nature Methods

Reviewing Activities

Ad hoc referee for the following peer reviewed journals: ACS Medicinal Chemistry Letters. Bioinformatics, Journal of Structural Biology, Journal of Medicinal Chemistry, Journal of Chemical Information & Modeling, Journal of Cheminformatics, Molecular Informatics, Nature Methods

Other Activities

Founder of Camball annual classic rally (2012 – Present; www.camball.eu)

Crew at checkpoint Amsterdam for Gumball 3000 rally (2010 – 2015)

Founder of “Lug-dunum Machra Alumni Association” (2009 – Present; Secretary 2009-2012)

Member of appointing committee for Professor van de Water at the department of Toxicology at the LACDR (2005)

Founder and member of fraternity “Lug-dunum Machra” (2002 – 2008; Vice-President 2002, Treasurer 2004, President 2005)

Member of student association A.L.S.V. “Quintus” (2002 – Present)

Member of the Leiden Pharmaceutical Students Association „Aesculapius” (2001 – 2007; President 2004)

Attachment: publications list

Articles in peer-reviewed journals:

Shardul Paricharak, Oscar Méndez-Lucio, Aakash Chavan Ravindranath, Andreas Bender, Adriaan P. IJzerman, and Gerard J. P. van Westen, Data-driven approaches used for compound library design, hit triage, and bioactivity modeling in high-throughput screening, Brief. Bioinform., 2016, In Press.

Eelke B. Lenselink, Willem Jespers, Herman W.T. Van Vlijmen, Adriaan P. IJzerman, and Gerard J.P. van Westen, Interacting with GPCRs; on the use of Interaction Fingerprints for Virtual Screening, JCIM, 2016, doi:10.1021/acs.jcim.6b00314

Serge Christmann-Franck, Gerard J.P. van Westen, George Papadatos, Fanny Beltran Escudie, Alexander Roberts, John P. Overington, and Daniel Domine, Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound–Kinase Activities: A Way toward Selective Promiscuity by Design?, JCIM, 56 (9), 1654-1675, 2016, doi: 10.1021/acs.jcim.6b00122

Isidro Cortés-Ciriano, Gerard J.P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, and Thérèse E. Malliavin, Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel, Bioinformatics (in press), 2015

Daniel S. Murrell, Isidro Cortes-Ciriano, Gerard J.P. van Westen, Ian Stott, Andreas Bender, Therese E. Malliavin, and Robert C., Glen Chemically Aware Model Builder (camb): An R package for property and bioactivity modelling of small molecules, Journal of Cheminf. (in press), 2015

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, A large-scale crop protection bioassay data set, Scientific Data 2, 150032, 2015, doi: 10.1038/sdata.2015.32

Grace Mugumbate, Katherine A. Abrahams, Jonathan A.G. Cox, George Papadatos, Gerard J.P. van Westen, Joel Lelievre, Szymon T. Calus, Nick Loman, Lluis Ballell, David Barros, John P. Overington, and Gurdyal S. Besra, Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation, PLoS ONE, 10(3), e0121492, 2015, doi:10.1371/journal.pone.0121492

P. Li, D. Rial, P. M Canas, J-H Yoo, W. Li, X Zhou, Y. Wang, Gerard J.P. 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, Optogenetic activation of intracellular adenosine A2A receptor signaling in the hippocampus is sufficient to trigger CREB phosphorylation and impair memory, Mol. Psychiatry, In press, 2015, doi:10.1038/mp.2014.182

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 J.P. van Westen, NCI-DREAM Community, Daniel Gallahan, Dinah Singer, Julio Saez-Rodriguez, Yang Xie, Gustavo Stolovitzky, and Andrea Califano, A community computational challenge to predict the activity of pairs of compounds, Nature Biotech 32, 2014, doi:10.1038/nbt.3052

Isidro Cortes-Ciriano, Daniel S. Murrell, Gerard J.P. van Westen, Andreas Bender, and Thérèse E. Malliavin, Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modelling, J. Cheminf, 7 (1), 2015, doi:10.1186/s13321-014-0049-z

Isidro Cortes-Ciriano, Qurrat U. Ain, Vigneshwari Subramanian, Eelke B. Lenselink, Oscar Mendez-Lucio, Adriaan P. IJzerman, Gerd Wohlfahrt, Peteris Prusis, Thérèse E. Malliavin, Gerard J.P. van Westen, Andreas Bender, Polypharmacology Modelling Using Proteochemometrics (PCM): Recent Methodological Developments, Applications to Target Families, and Future Prospects, MedChemComm 6, 24-50, 2015, doi: 10.1039/C4MD00216D

Mark Davies, Michał Nowotka, George Papadatos, Francis Atkinson, Gerard J.P. van Westen, Nathan Dedman, Rodrigo Ochoa, John P. Overington, MyChEMBL: A Virtual Platform for Distributing Cheminformatics Tools and Open Data, Challenges, 5 (2), 334-337, 2014

Qurrat U. Ain, Oscar Méndez-Lucio, Isidro Cortés Ciriano, Thérèse Malliavin, Gerard JP van Westen, and Andreas Bender, Modelling ligand selectivity of Serine Proteases using integrative Proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features, Integrative Biol., 6, 1023-1033, 2014, doi: 10.1039/C4IB00175C

Miriam C. Peeters, Qilan Li, Rachel Elands, Gerard J.P. van Westen, Eelke B. Lenselink, Christa E. Müller, and Adriaan P. IJzerman, Domains for activation and inactivation in G protein-coupled receptors–a mutational analysis of constitutive activity of the adenosine A2B receptor, Biochem. Pharmacol., 92 (2), 348–357, 2014, doi:10.1016/j.bcp.2014.08.022

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, and Andy Simmons, Random Forest ensembles for detection and prediction of Alzheimers Disease with a good between-cohort robustness, Neuroimage: Clinical, 6, 115-125, 2014, doi: 10.1016/j.nicl.2014.08.023

George Papadatos, Gerard J.P. van Westen, Samuel Croset, Rita Santos, Simone Trubian and John P. Overington, A document classifier for medicinal chemistry publications trained on the ChEMBL corpus, J Cheminform, 6, 40, 2014, doi:10.1186/s13321-014-0040-8

Irina Kufareva, Vsevolod Katritch, Participants of GPCR Dock2013 (Gerard J.P. van Westen), Raymond C. Stevens, Ruben Abagyan, Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges, Structure, 22 (8), 1120-1139, 2014, doi:10.1016/j.str.2014.06.012

Isidro Cortes-Ciriano, Gerard J.P. van Westen, Eelke B. Lenselink, Daniel S. Murrell, Andreas Bender and Thérèse Malliavin, Proteochemometric modeling in a Bayesian framework, J Cheminform., 6, 35, 2014, doi:10.1186/1758-2946-6-35

Costello, James C., Laura M. Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P. Menden, Nicholas J. Wang, Gerard J.P. van Westen, Mukesh Bansal et al. A community effort to assess and improve drug sensitivity prediction algorithms, Nature Biotech, 32, 1202–1212, 2014, doi:10.1038/nbt.2877

Gerard J.P. van Westen, Andreas Bender, John P Overington, Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modeling, Journal of Chem Biol., 7 (4), 119-123, 2014, doi:10.1007/s12154-014-0112-2

Gerard J.P. van Westen, Anna Gaulton, John P Overington, Chemical, Target, and Bioactive Properties of Allosteric Modulation, PLoS Comp. Biol., 10 (4), e1002899, 2014, doi:10.1371/journal.pcbi.1003559

Gerard J.P. van Westen, Remco F Swier, Isidro Cortes-Ciriano, Jörg K Wegner,John P Overington,Adriaan P IJzerman, Herman WT van Vlijmen, Andreas Bender; Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets, J Cheminform., 5, 42, 2013, doi:10.1186/1758-2946-5-42

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

Tom De Bruyn, Gerard J.P. van Westen, Adriaan P. IJzerman, Bruno Stieger, Peter de Witte, Patrick F. Augustijns, Pieter P. Annaert, Structure-based identification of OATP1B1/3 inhibitors, Mol. Pharmacol., 83, 1257-1267, 2013, doi:10.1124/mol.112.084152

Gerard J.P.van Westen and John P. Overington, A ligand’s-eye view of protein similarity, Nat. methods, 10, 116-117, 2013, doi:10.1038/nmeth.2339

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 Comp. Biol., 9 (2), e1002899, 2013, doi: 10.1371/journal.pcbi.1002899

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, Andreas Bender; Identifying Novel Adenosine Receptor Ligands by Simultaneous Proteochemometric Modeling of Rat and Human Bioactivity Data, J. Med. Chem., 55 (16), 7010-7020, 2012, doi: 10.1021/jm3003069

Robert Lane, Carmen Klein Herenbrink, Gerard J.P. van Westen, Jelle A. Spoorendonk, Carsten Hoffman, Adriaan P. IJzerman; A Novel Non-ribose Agonist, LUF5834, Engages Distinct Residues from that of Adenosine-like Ligands to Activate the Adenosine A2A Receptor, Mol. Pharmacol., 8 (3), 475-487, 2012, doi: 10.1124/mol.111.075937

Gerard J.P. van Westen, Jörg K. Wegner, Peggy Geluykens, Leen Kwanten, Inge Vereycken, Anik Peeters, Adriaan P. IJzerman, Herman W.T. van Vlijmen, Andreas Bender; Which Compound to Select in Lead Optimization? Prospectively Validated Proteochemometric Models Guide Preclinical Development, PLoS ONE, 6 (11), e27518, 2012, doi: 10.1371/journal.pone.0027518

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

Miriam C. Peeters, Gerard J.P. van Westen, Dong Guo, Lisanne. E. Wisse, Christa. E. Müller, Margot W. Beukers, Adriaan P. IJzerman; GPCR structure and activation: an essential role for the first extracellular loop in activating the adenosine A2B receptor, FASEB J., 25 (2), 632-643, 2011, doi: 10.1096/fj.10-164319

Miriam C. Peeters, Gerard J.P. van Westen, Qilan Li, Adriaan P. Ijzerman; The importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation, TiPS, 32 (1), 35-42, 2011, doi: 10.1016/j.tips.2010.10.001

Gerard J.P. van Westen, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender; Proteochemometric Modeling as a Tool to Design Selective Compounds and for Extrapolating to Novel Targets, Med. Chem. Commun., 2, 16-30, 2011, doi: 10.1039/C0MD00165A

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; Chemogenomics Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space, Curr. Top. Med. Chem. 11 (15), 1964-1977, 2011, doi: 10.2174/156802611796391230

Gerard J.P. van Westen, Jörg K. Wegner, Andreas Bender, Adriaan P. IJzerman, Herman W. T. van Vlijmen; Mining protein dynamics from sets of crystal structures using "consensus structures", Prot. Sci., 19 (4), 742-752, 2010, doi: 10.1002/pro.350

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 Mining, 2 (3), 149 – 160, 2009, doi: 10.1002/sam.10046

Selected presentations

Unilever R&D (Vlaardingen, The Netherlands), March 2015 (Talk, invited)

LACDR Fall Symposium 2014 (Leiden, the Netherlands), October 2015 (Talk, invited)

Syngenta R&D Lunch Seminar (Bracknell, United Kingdom), November 2014 (Talk, invited)

Unilever R&D (Bedford, UK), May 2014 (Talk, invited)

10^th International Conference on Chemical Structures 2014 (Noordwijkerhout, The Netherlands), June 2014 (Talk, contributed)

KNCV Medicinal Chemistry Spring Symposium 2014 (Utrecht, The Netherlands), March 2014 (Talk, invited)

FIGON Dutch Medicines Days 2013 (Ede, The Netherlands), October 2013 (Talk, invited)

Dutch Computers in Science Symposium (Amsterdam (KNAW)), The Netherlands, July 2013 (Talk, invited)

Heptares invited Lecture (Welwyn Garden City, UK), February 2013 (Talk, invited)

Edingburgh Meeting on Allostery (Edingburg, UK), December 2012 (Talk, invited)

Cambridge Cheminformatics Network Meeting (Cambridge, UK), August 2012 (Talk, invited)

Molsoft ICM User Group Meeting 2012 (San Diego, USA), March 2012 (Talk, invited)

FIGON Dutch Medicines Days 2011 (Lunteren, The Netherlands), October 2011 (Talk, invited)

ULLA Summer School (Parma, Italy), July 2011 (Talk, contributed)

TI-Pharma GPCR Forum Workshop (Driebergen, The Netherlands), June 2011 (Talk, invited)

9^th International Conference on Chemical Structures (Noordwijkerhout, The Netherlands), June 2011 (Talk, contributed)

FIGON Dutch Medicines Days 2010 (Lunteren, The Netherlands), October 2010 (Talk, invited)

EuroQSAR 2010 (Rhodes, Greece), September 2010 (Talk, contributed)

5^th German Conference on Cheminformatics (Goslar, Germany), November 2009 (Talk, contributed)

FIGON Dutch Medicines Days 2009 (Lunteren, The Netherlands), October 2009 (Poster, contributed)

FIGON Dutch Medicines Days 2008 (Lunteren, The Netherlands), October 2008 (Poster, contributed)

EuroQSAR 2008 (Uppsala, Sweden), September 2008 (Poster, contributed)

8^th International Conference on Chemical Structures (Noordwijkerhout, The Netherlands), June 2008 (Poster, contributed)

Virtual Discovery Europe (Amsterdam, The Netherlands), July 2008 (Talk, contributed)