SheeP: A tool for description of beta-sheets in protein 3D structuresстатья
Информация о цитировании статьи получена из
Web of Science
Статья опубликована в журнале из списка Web of Science и/или Scopus
Дата последнего поиска статьи во внешних источниках: 31 октября 2012 г.
Аннотация: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 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.