News and Updates


2019_04_12 Quite a few publications added...

posted Apr 12, 2019, 7:43 AM by Gerard van Westen   [ updated Apr 12, 2019, 10:12 PM ]


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 


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 


 
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 

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: 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

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: 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

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

2014-09-16

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

2014-07-28

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    
   
    

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