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Cited by 408

The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.

Validation Studies of the Site-Directed Docking Program LibDock

Open access
Rao, Shashidhar N., Head, Martha S., Kulkarni, Amit, LaLonde, Judith M.·2007·Journal of Chemical Information and Modeling
DOI 10.1021/ci6004299
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Abstract

The performance of the site-features docking algorithm LibDock has been evaluated across eight GlaxoSmithKline targets as a follow-up to a broad validation study of docking and scoring software (Warren, G. L.; Andrews, W. C.; Capelli, A.; Clarke, B.; Lalonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Walls, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. J. Med. Chem. 2006, 49, 5912-5931). Docking experiments were performed to assess both the accuracy in reproducing the binding mode of the ligand and the retrieval of active compounds in a virtual screening protocol using both the DJD (Diller, D. J.; Merz, K. M., Jr. Proteins 2001, 43, 113-124) and LigScore2 (Krammer, A. K.; Kirchoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. J. Mol. Graphics Modell. 2005, 23, 395-407) scoring functions. This study was conducted using DJD scoring, and poses were rescored using all available scoring functions in the Accelrys LigandFit module, including LigScore2. For six out of eight targets at least 30% of the ligands were docked within a root-mean-square difference (RMSD) of 2.0 A for the crystallographic poses when the LigScore2 scoring function was used. LibDock retrieved at least 20% of active compounds in the top 10% of screened ligands for four of the eight targets in the virtual screening protocol. In both studies the LigScore2 scoring function enhanced the retrieval of crystallographic poses or active compounds in comparison with the results obtained using the DJD scoring function. The results for LibDock accuracy and ligand retrieval in virtual screening are compared to 10 other docking and scoring programs. These studies demonstrate the utility of the LigScore2 scoring function and that LibDock as a feature directed docking method performs as well as docking programs that use genetic/growing and Monte Carlo driven algorithms.

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Metadata

Authors
Rao, S. N., Head, M. S., Kulkarni, A., & LaLonde, J. M.
Venue
Journal of Chemical Information and Modeling
Publisher
American Chemical Society (ACS)
Published
2007-11-01
Volume
47
Issue
6
Pages
2159-2171
ISSN
  • 1549-9596 (ISSN-L)
  • 1549-960X
DOI
10.1021/ci6004299
OpenAlex
W1975623001
Cited by
408
References
45
FWCI
3.04
Type
journal article
Language
en
Open access
hybrid

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