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Diverse, high-quality test set for the validation of protein-ligand docking performance.

Abstract：

:A procedure for analyzing and classifying publicly available crystal structures has been developed. It has been used to identify high-resolution protein-ligand complexes that can be assessed by reconstructing the electron density for the ligand using the deposited structure factors. The complexes have been clustered according to the protein sequences, and clusters have been discarded if they do not represent proteins thought to be of direct interest to the pharmaceutical or agrochemical industry. Rules have been used to exclude complexes containing non-drug-like ligands. One complex from each cluster has been selected where a structure of sufficient quality was available. The final Astex diverse set contains 85 diverse, relevant protein-ligand complexes, which have been prepared in a format suitable for docking and are to be made freely available to the entire research community (http://www.ccdc.cam.ac.uk). The performance of the docking program GOLD against the new set is assessed using a variety of protocols. Relatively unbiased protocols give success rates of approximately 80% for redocking into native structures, but it is possible to get success rates of over 90% with some protocols.

journal_name

J Med Chem

journal_title

Journal of medicinal chemistry

authors

Hartshorn MJ,Verdonk ML,Chessari G,Brewerton SC,Mooij WT,Mortenson PN,Murray CW

doi

10.1021/jm061277y

subject

Has Abstract

pub_date

2007-02-22 00:00:00

pages

726-41

issue

4

eissn

0022-2623

issn

1520-4804

journal_volume

50

pub_type

杂志文章

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