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Knowledge-based protein secondary structure assignment (1995)
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| Venue: | Proteins |
| Citations: | 324 - 2 self |
BibTeX
@ARTICLE{Frishman95knowledge-basedprotein,
author = {Dmitrij Frishman and Patrick Argos},
title = {Knowledge-based protein secondary structure assignment},
journal = {Proteins},
year = {1995},
volume = {23},
pages = {566--579}
}
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Abstract
ABSTRACT We have developed an auto-matic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone tor-sional angle information. Parameters of the pattern recognition procedure were optimized using designations provided by the crystallog-raphers as a standard-of-truth. Comparison to the currently most widely used technique DSSP by Kabsch and Sander (Biopolymers 222577-2637, 1983) shows that STRIDE and DSSP as-sign secondary structural states in 58 and 31% of 226 protein chains in our data sample, re-spectively, in greater agreement with the spe-cific residue-by-residue definitions provided by the discoverers of the structures while in 11 % of the chains, the assignments are the same. STRIDE delineates every 11 th helix and every 32nd strand more in accord with published assignments. Q 1995 Wiley-Liss, Inc. Key words: protein structure analysis, hydro-gen bond, torsional angle, a-helix, p-sheet
Keyphrases
knowledge-based protein secondary structure assignment spe-cific residue-by-residue definition backbone tor-sional angle information key word hydrogen bond energy atomic coordinate hydro-gen bond published assignment th helix protein secondary structure assignment torsional angle pattern recognition procedure data sample auto-matic algorithm stride protein structure analysis protein chain technique dssp dssp as-sign secondary structural state
