posted Apr 12, 2019, 7:43 AM by Gerard van Westen
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updated Apr 12, 2019, 10:12 PM
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49 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
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48 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
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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
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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
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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
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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
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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
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posted Feb 1, 2018, 6:46 AM by Gerard van Westen
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
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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
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posted Nov 14, 2017, 1:26 PM by Gerard van Westen
40 Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms
TiPS (2018), accepted
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
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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
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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
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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
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posted Mar 21, 2017, 9:40 AM by Gerard van Westen
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
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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
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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
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posted Aug 27, 2015, 2:15 AM by Gerard van Westen
33 Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel
Bioinformatics (2015), in press
Isidro Cortés-Ciriano, Gerard J.P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, and Thérèse E. Malliavin
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32 Chemically Aware Model Builder (camb): An R package for property and bioactivity modelling of small molecules
Journal of Cheminformatics (2015), in press
Daniel S. Murrell, Isidro Cortes-Ciriano, Gerard J.P. van Westen, Ian Stott, Andreas Bender, Therese E. Malliavin, and Robert C. Glen
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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
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posted Mar 2, 2015, 2:40 AM by Gerard van Westen
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updated Mar 25, 2015, 1:23 AM
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30 Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validationphosphorylation and impair memory
PLoS ONE (2015) In press doi:n/a
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
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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
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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
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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
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posted Oct 8, 2014, 3:33 AM by Gerard van Westen
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
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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
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posted Sep 16, 2014, 1:55 AM by Gerard van Westen
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updated Sep 18, 2014, 1:54 AM
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4 new publications added! :)
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
Qurrat U Ain, Oscar Méndez-Lucio, Isidro Cortés Ciriano, Thérèse Malliavin, Gerard JP van Westen, and Andreas Bender
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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
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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
Miriam C. Peeters, Qilan Li, Rachel Elands, Gerard J.P. van Westen, Eelke B. Lenselink, Christa E. Müller, Adriaan P. IJzerman
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21 Random Forest ensembles for detection and prediction of Alzheimer's Disease with a good between-cohort robustness
Neuroimage: Clinical (2014) 6 115–125 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
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posted Jul 28, 2014, 6:30 AM by Gerard van Westen
New publication!
20 A document classifier for medicinal chemistry publications trained on the ChEMBL corpus
Journal of Cheminformatics (2014) In Press
George Papadatos, Gerard J.P. van Westen, Samuel Croset, Rita Santos, Simone Trubian and John P. Overington
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posted Jun 30, 2014, 1:25 AM by Gerard van Westen
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