SHEEP: A TOOL FOR DESCRIPTION OF β-SHEETS IN PROTEIN 3D STRUCTURES

The description of a protein fold is a hard problem due to significant variability of main structural units, beta-sheets and alpha-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 beta-sheets than for alpha-helixes due to beta-sheets variability both in composition and geometry. We have developed an algorithm that can significantly modify beta-sheets detected by commonly used DSSP and Stride algorithms and represent the result as a "beta-sheet map," a table describing certain beta-sheet features. In our approach, beta-sheets (rather than beta-strands) are considered as holistic objects. Both hydrogen bonds and geometrical restrains are explored for the determination of beta-sheets. The algorithm is implemented in SheeP program. It was tested for prediction architectures of domains from 93 well-defined all-beta and alpha/beta SCOP protein domain families, and showed 93% of correct results. The Web-service http://mouse.belozersky.msu.ru/sheep allows to detect beta-sheets in a given protein structure, visualize beta-sheet maps, as well as input three-dimensional structures with highlighted beta-sheets and their structural features.