Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks.

Autor: Georgi K Kanev, Yaran Zhang, Albert J Kooistra, Andreas Bender, Rob Leurs, David Bailey, Thomas Würdinger, Chris de Graaf, Iwan J P de Esch, Bart A Westerman

Publikováno v: PLoS Computational Biology, Vol 19, Iss 9, p e1011301 (2023)

Many therapies in clinical trials are based on single drug-single target relationships. To further extend this concept to multi-target approaches using multi-targeted drugs, we developed a machine learning pipeline to unravel the target landscape of

Externí odkaz: https://doaj.org/article/3875d0fdcc1341ac8c4a8184e67a02c7

KLIFS

Autor: Iwan J. P. de Esch, Chris de Graaf, Albert J. Kooistra, Bart A. Westerman, Georgi K. Kanev

Publikováno v: Kanev, G K, de Graaf, C, Westerman, B A, de Esch, I J P & Kooistra, A J 2021, ' KLIFS : an overhaul after the first 5 years of supporting kinase research ', Nucleic acids research, vol. 49, no. D1, pp. D562-D569 . https://doi.org/10.1093/nar/gkaa895
Nucleic Acids Research
Kanev, G K, de Graaf, C, Westerman, B A, de Esch, I J P & Kooistra, A J 2021, ' KLIFS : an overhaul after the first 5 years of supporting kinase research ', Nucleic Acids Research, vol. 49, no. D1, pp. D562-D569 . https://doi.org/10.1093/nar/gkaa895
Nucleic Acids Research, 49(D1), D562-D569. Oxford University Press
Nucleic acids research, 49(D1), D562-D569. Oxford University Press

Kinases are a prime target of drug development efforts with >60 drug approvals in the past two decades. Due to the research into this protein family, a wealth of data has been accumulated that keeps on growing. KLIFS—Kinase–Ligand Interaction Fin

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aed2f7dd0777f5c73b8e9a26f6c1033b
http://www.scopus.com/inward/record.url?scp=85099428687&partnerID=8YFLogxK

Structural Chemogenomics Databases to Navigate Protein–Ligand Interaction Space

Autor: Georgi K. Kanev, I.J.P. de Esch, C de Graaf, Albert J. Kooistra

Structural chemogenomics databases allow the integration and exploration of heterogeneous genomic, structural, chemical, and pharmacological data in order to extract useful information that is applicable for the discovery of new protein targets and b

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::d9bfdac8547123c9f09a2b8341cd82a5
https://doi.org/10.1016/b978-0-12-409547-2.12298-x

PDEStrIAn: A phosphodiesterase structure and ligan interaction annotated database as a tool for structure-based drug design

Autor: Albert J. Kooistra, Chris de Graaf, Iwan J. P. de Esch, Chimed Jansen, Georgi K. Kanev, Rob Leurs

Publikováno v: Journal of Medicinal Chemistry, 59(15), 7029-7065. American Chemical Society
Jansen, C J W, Kooistra, A J, Kanev, G K, Leurs, R, de Esch, I J P & de Graaf, C 2016, ' PDEStrIAn: A phosphodiesterase structure and ligan interaction annotated database as a tool for structure-based drug design. ', Journal of Medicinal Chemistry, vol. 59, no. 15, pp. 7029-7065 . https://doi.org/10.1021/acs.jmedchem.5b01813

A systematic analysis is presented of the 220 phosphodiesterase (PDE) catalytic domain crystal structures present in the Protein Data Bank (PDB) with a focus on PDE-ligand interactions. The consistent structural alignment of 57 PDE ligand binding sit

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::748d97fb21984b9f27ae46d50e996834
https://research.vu.nl/en/publications/4fbe05eb-49ab-4e58-8113-65751a7e03d7

To Target or Not to Target Schistosoma mansoni Cyclic Nucleotide Phosphodiesterase 4A?

Autor: Zheng, Yang¹ (AUTHOR) y.zheng@vu.nl, Schroeder, Susanne² (AUTHOR) s.schroeder.uk@gmail.com, Kanev, Georgi K.¹ (AUTHOR) gkkanev@gmail.com, Botros, Sanaa S.³ (AUTHOR) sanaabotros113@gmail.com, William, Samia⁴ (AUTHOR) samiaw2006@yahoo.com, Sabra, Abdel-Nasser A.³ (AUTHOR) abdelnassersabraa@yahoo.com, Maes, Louis⁵ (AUTHOR) louis.maes@uantwerpen.be, Caljon, Guy⁵ (AUTHOR) guy.caljon@uantwerpen.be, Gil, Carmen⁶ (AUTHOR) carmen.gil@csic.es, Martinez, Ana⁶ (AUTHOR) ana.martinez@csic.es, Salado, Irene G.⁷ (AUTHOR) irenegarciasalado@gmail.com, Augustyns, Koen⁷ (AUTHOR) koen.augustyns@uantwerpen.be, Edink, Ewald¹ (AUTHOR) ewald.edink@inholland.nl, Sijm, Maarten¹ (AUTHOR) sijm.maarten@gmail.com, de Heuvel, Erik¹ (AUTHOR) erikdeheuvel8@gmail.com, de Esch, Iwan J. P.¹ (AUTHOR) i.de.esch@vu.nl, van der Meer, Tiffany¹ (AUTHOR) t.k.vander.meer@vu.nl, Siderius, Marco¹ (AUTHOR) m.siderius@vu.nl, Sterk, Geert Jan¹ (AUTHOR) g.j.sterk@vu.nl, Brown, David² (AUTHOR) david.brown@servier.com

Publikováno v: International Journal of Molecular Sciences. Apr2023, Vol. 24 Issue 7, p6817. 18p.