Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 26, Issue 11, Pages 1189-1192Publisher
WILEY
DOI: 10.1002/jcc.20251
Keywords
decoy clustering; near-native detection; root-mean-squared distance
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Funding
- NIGMS NIH HHS [R01 GM 068530, R01 GM 966049] Funding Source: Medline
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We developed a method for fast decoy clustering by using reference root-mean-squared distance (rRMSD) rather than commonly used pairwise RMSD (pRMSD) values. For 41 proteins with 2000 decoys each, the computing efficiency increases nine times without a significant change in the accuracy of near-native selections. Tests on additional protein decoys based on different reference conformations confirmed this result. Further analysis indicates that the pRMSD and rRMSD values are highly correlated (with an average correlation coefficient of 0.82) and the clusters obtained from pRMSD and rRMSD values are highly similar (the representative structures of the top five largest clusters from the two methods are 74% identical). SCUD (Structure ClUstering of Decoys) with an automatic cutoff value is available at http://theory.med.buffalo.edu. (c) 2005 Wiley Periodicals, Inc.
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