DSSPcont: continuous secondary structure assignments for proteins

被引:90
作者
Carter, P
Andersen, CAF
Rost, B
机构
[1] Columbia Univ, Dept Biochem & Mol Biophys, CUBIC, New York, NY 10032 USA
[2] Columbia Univ, Dept Biochem & Mol Biophys, NE Struct Genom Consortium, New York, NY 10032 USA
[3] BASF AG, D-67056 Ludwigshafen, Germany
[4] Univ London Imperial Coll Sci Technol & Med, Dept Biol Sci, Struct Bioinformat Grp, London, England
[5] Columbia Univ, Ctr Computat Biol & Bioinformat, New York, NY 10032 USA
关键词
D O I
10.1093/nar/gkg626
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.columbia.edu/services/DSSPcont) introduces a continuous assignment of secondary structure that replaces 'static' by 'dynamic' states. Technically, the continuum results from calculating weighted averages over 10 discrete DSSP assignments with different hydrogen bond thresholds. A DSSPcont assignment for a particular residue is a percentage likelihood of eight secondary structure states, derived from a weighted average of the ten DSSP assignments. The continuous assignments have two important features: (i) they reflect the structural variations due to thermal fluctuations as detected by NMR spectroscopy; and (ii) they reproduce the structural variation between many NMR models from one single model. Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure.
引用
收藏
页码:3293 / 3295
页数:3
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