SCUD : fast structure clustering of decoys using reference state to remove overall rotation
(c) 2005 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 26(2005), 11 vom: 24. Aug., Seite 1189-92 |
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| Format: | Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2005
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Proteins |
| Zusammenfassung: | (c) 2005 Wiley Periodicals, Inc. 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 |
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| Beschreibung: | Date Completed 28.07.2005 Date Revised 14.11.2007 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |