NDLI: 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

Content Provider	Springer Nature Link
Author	Repasky, Matthew P. Murphy, Robert B. Banks, Jay L. Greenwood, Jeremy R. Tubert Brohman, Ivan Bhat, Sathesh Friesner, Richard A.
Copyright Year	2012
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 enrichment to DUD best-practices Glide SP results.
Starting Page	787
Ending Page	799
Page Count	13
File Format	PDF
ISSN	0920654X
Journal	Journal of Computer-Aided Molecular Design
Volume Number	26
Issue Number	6
e-ISSN	15734951
Language	English
Publisher	Springer Netherlands
Publisher Date	2012-05-11
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Docking Virtual screening DUD Astex WScore WaterMap Glide Animal Anatomy / Morphology / Histology Computer Applications in Chemistry Physical Chemistry
Content Type	Text
Resource Type	Article
Subject	Drug Discovery Physical and Theoretical Chemistry Computer Science Applications

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