Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide.

Journal of Computer-aided Molecular Design
Matthew P RepaskyRichard A Friesner

Abstract

Glide SP mode enrichment results for two preparations of the DUD dataset and native ligand docking RMSDs for two preparations of the Astex dataset are presented. Following a best-practices preparation scheme, an average RMSD of 1.140 Å for native ligand docking with Glide SP is computed. Following the same best-practices preparation scheme for the DUD dataset an average area under the ROC curve (AUC) of 0.80 and average early enrichment via the ROC (0.1 %) metric of 0.12 were observed. 74 and 56 % of the 39 best-practices prepared targets showed AUC over 0.7 and 0.8, respectively. Average AUC was greater than 0.7 for all best-practices protein families demonstrating consistent enrichment performance across a broad range of proteins and ligand chemotypes. In both Astex and DUD datasets, docking performance is significantly improved employing a best-practices preparation scheme over using minimally-prepared structures from the PDB. Enrichment results for WScore, a new scoring function and sampling methodology integrating WaterMap and Glide, are presented for four DUD targets, hivrt, hsp90, cdk2, and fxa. WScore performance in early enrichment is consistently strong and all systems examined show AUC > 0.9 and superior early enrich...Continue Reading

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Citations

Apr 13, 2013·Journal of Computer-aided Molecular Design·G Madhavi SastryWoody Sherman
Oct 3, 2013·Journal of Medicinal Chemistry·Jayendra Z PatelTapio Nevalainen
Oct 10, 2013·Journal of Medicinal Chemistry·Venkata Ramana SirivoluZhengqiang Wang
Oct 18, 2013·Journal of Medicinal Chemistry·Giuseppe ManfroniVioletta Cecchetti
Feb 8, 2014·Journal of Computer-aided Molecular Design·Emilio GallicchioRonald M Levy
Jun 3, 2014·Journal of Cheminformatics·Ali AhmedAmmar Abdo
Jul 6, 2014·Journal of Computer-aided Molecular Design·Angela M HenzlerMatthias Rarey
Oct 9, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Mohammed Mumtaz Al-DabbaghFaisal Saeed
Jun 22, 2012·Journal of Medicinal Chemistry·Michael M MysingerBrian K Shoichet
Jul 8, 2015·Journal of Chemical Information and Modeling·Brian P KelleySteven W Muchmore
Feb 26, 2016·Journal of Medicinal Chemistry·John J Irwin, Brian K Shoichet
Mar 10, 2016·Journal of Chemical Information and Modeling·Dahlia R WeissJonathan S Mason
Mar 19, 2016·Protein Science : a Publication of the Protein Society·Orly DymIsrael Silman
Mar 27, 2015·Journal of Molecular Recognition : JMR·Elizabeth YurievPaul A Ramsland
Jun 1, 2015·Molecular Informatics·Lucía Serrán-AguileraRamón Hurtado-Guerrero
May 6, 2015·Journal of Computer-aided Molecular Design·Ann E Cleves, Ajay N Jain
Apr 30, 2013·European Journal of Medicinal Chemistry·Miriam CorredorAngel Messeguer
Jan 1, 2013·Computational and Structural Biotechnology Journal·Valère LounnasNicolas Foloppe
Apr 8, 2016·Journal of Medicinal Chemistry·Robert B MurphyRichard A Friesner
Mar 3, 2015·Journal of Computer-aided Molecular Design·Emilio GallicchioRonald M Levy
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Nov 20, 2013·Journal of Chemical Information and Modeling·Rafał Kurczab, Andrzej J Bojarski
Nov 6, 2012·Journal of Chemical Information and Modeling·Thijs Beuming, Woody Sherman
Nov 20, 2012·Journal of Chemical Information and Modeling·Haipeng Hu, James P Snyder
Dec 14, 2011·Journal of Chemical Information and Modeling·Fredrik SvenssonChristian Sköld
Mar 28, 2012·Journal of Chemical Information and Modeling·Emanuele PerolaJonathan Weiss
Oct 15, 2013·Journal of Chemical Information and Modeling·Akos TarcsayGyörgy M Keserű
May 3, 2014·Journal of Chemical Information and Modeling·Anna Lucia FallacaraMaurizio Botta
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Jul 6, 2017·Journal of Chemical Information and Modeling·Yuna YanChangge Ji
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