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Benchmarking Sets for Molecular Docking

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Department of Pharmaceutical Chemistry, University of California San Francisco, QB3 Building, 1700 4th Street, Box 2550, San Francisco, California 94143-2550
Cite this: J. Med. Chem. 2006, 49, 23, 6789–6801
Publication Date (Web):October 26, 2006
https://doi.org/10.1021/jm0608356
Copyright © 2006 American Chemical Society
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    Abstract

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    Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 98 266 compounds. For most targets, enrichment was at least half a log better with uncorrected databases such as the MDDR than with DUD, evidence of bias in the former. These calculations also allowed 40 × 40 cross-docking, where the enrichments of each ligand set could be compared for all 40 targets, enabling a specificity metric for the docking screens. DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/.

    *

     To whom correspondence should be addressed. B.K.S:  phone, 415-514-4126; fax, 415-514-4260; E-mail, [email protected]. J.J.I:  phone, 415-514-4127; fax, 415-514-4260; e-mail, [email protected].

    Abbreviations:  DUD, directory of useful decoys; EF, enrichment factor; MDDR, MDL Drug Data Report; Tc, Tanimoto coefficient; ROC, receiver operating characteristic; ACE, angiotensin-converting enzyme; AChE, acetylcholinesterase; ADA, adenosine deaminase; ALR2, aldose reductase; AmpC, AmpC β-lactamase; AR, androgen receptor; CDK2, cyclin-dependent kinase 2; COMT, catechol O-methyltransferase; COX-1, cyclooxygenase-1; COX-2, cyclooxygenase-2; DHFR, dihydrofolate reductase; EGFr, epidermal growth factor receptor; ER, estrogen receptor; FGFr1, fibroblast growth factor receptor kinase; FXa, factor Xa; GART, glycinamide ribonucleotide transformylase; GPB, glycogen phosphorylase β; GR, glucocorticoid receptor; HIVPR, HIV protease; HIVRT, HIV reverse transcriptase; HMGR, hydroxymethylglutaryl-CoA reductase; HSP90, human heat shock protein 90; InhA, enoyl ACP reductase; MR, mineralocorticoid receptor; NA, neuraminidase; P38 MAP, P38 mitogen activated protein; PARP, poly(ADP-ribose) polymerase; PDE5, phosphodiesterase 5; PDGFrb, platelet derived growth factor receptor kinase; PNP, purine nucleoside phosphorylase; PPARg, peroxisome proliferator activated receptor γ; PR, progesterone receptor; RXRa, retinoic X receptor α; SAHH, S-adenosyl-homocysteine hydrolase; SRC, tyrosine kinase SRC; TK, thymidine kinase; VEGFr2, vascular endothelial growth factor receptor; ATP, adenosine-5‘-triphosphate; β-GAR, β-glycinamide ribonucleotide; NAD(P)-(H), nicotinamide adenine dinucleotide (phosphate)-(reduced); PLP, pyridoxal-5‘-phosphate.

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    Schematic description of the automated docking pipeline, selected property distribution historgrams and 2D depictions of typical molecules for annotated ligands and their decoys, property distribution histograms of Rognan's ligands and decoys, enrichment plots comparing the semiautomated with the fully automated docking procedure, and complete listings of the modified parameter files used. This material is available free of charge via the Internet at http://pubs.acs.org.

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