News and Updates

2018_02_01 New Publications added

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: 
        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: 
        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

2017_11_14 4 new publications added...

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 

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

2017_03_21 3 new publications added

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:
        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

2015-08-27 3 new publications added!

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

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

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

2015-03-02 4 new publications added...! :)

posted Mar 2, 2015, 2:40 AM by Gerard van Westen   [ updated Mar 25, 2015, 1:23 AM ]

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

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 

2014-10-08 Two more publications (probably last of 2014...)

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 

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


posted Sep 16, 2014, 1:55 AM by Gerard van Westen   [ updated Sep 18, 2014, 1:54 AM ]

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 

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 Pharmacolog(2014) In Press          
        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) 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


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    

2014-06-30 New Publication added

posted Jun 30, 2014, 1:25 AM by Gerard van Westen

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    

2014-06-13 New Publication added!

posted Jun 13, 2014, 3:30 AM by Gerard van Westen

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    

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