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J Bioinform Comput Biol. 2012 Apr;10(2):1241003. doi: 10.1142/S021972001241003X.

SheeP: A tool for description of β-sheets in protein 3D structures.

Author information

1
Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1-40, Moscow 119991, Russia. evaksianov@gmail.com

Abstract

The description of a protein fold is a hard problem due to significant variability of main structural units, β-sheets and α-helixes, and their mutual arrangements. An adequate description of the structural units is an important step in objective protein structure classification, which to date is based on expert judgment in a number of cases. Explicit determination and description of structural units is more complicated for β-sheets than for α-helixes due to β-sheets variability both in composition and geometry. We have developed an algorithm that can significantly modify β-sheets detected by commonly used DSSP and Stride algorithms and represent the result as a "β-sheet map," a table describing certain β-sheet features. In our approach, β-sheets (rather than β-strands) are considered as holistic objects. Both hydrogen bonds and geometrical restrains are explored for the determination of β-sheets. The algorithm is implemented in SheeP program. It was tested for prediction architectures of domains from 93 well-defined all-β and α/β SCOP protein domain families, and showed 93% of correct results. The Web-service allows to detect β-sheets in a given protein structure, visualize β-sheet maps, as well as input three-dimensional structures with highlighted β-sheets and their structural features.

PMID:
22809339
DOI:
10.1142/S021972001241003X
[Indexed for MEDLINE]

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