Kumar, Prasun and Bansal, Manju (2015) Identification of local variations within secondary structures of proteins. In: ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 71 (5). pp. 1077-1086.
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Abstract
Secondary-structure elements (SSEs) play an important role in the folding of proteins. Identification of SSEs in proteins is a common problem in structural biology. A new method, ASSP (Assignment of Secondary Structure in Proteins), using only the path traversed by the C atoms has been developed. The algorithm is based on the premise that the protein structure can be divided into continuous or uniform stretches, which can be defined in terms of helical parameters, and depending on their values the stretches can be classified into different SSEs, namely -helices, 3(10)-helices, -helices, extended -strands and polyproline II (PPII) and other left-handed helices. The methodology was validated using an unbiased clustering of these parameters for a protein data set consisting of 1008 protein chains, which suggested that there are seven well defined clusters associated with different SSEs. Apart from -helices and extended -strands, 3(10)-helices and -helices were also found to occur in substantial numbers. ASSP was able to discriminate non--helical segments from flanking -helices, which were often identified as part of -helices by other algorithms. ASSP can also lead to the identification of novel SSEs. It is believed that ASSP could provide a better understanding of the finer nuances of protein secondary structure and could make an important contribution to the better understanding of comparatively less frequently occurring structural motifs. At the same time, it can contribute to the identification of novel SSEs. A standalone version of the program for the Linux as well as the Windows operating systems is freely downloadable and a web-server version is also available at .
Item Type: | Journal Article |
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Publication: | ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY |
Publisher: | WILEY-BLACKWELL |
Additional Information: | Copy right for this article belongs to the WILEY-BLACKWELL, 111 RIVER ST, HOBOKEN 07030-5774, NJ USA |
Keywords: | ASSP; -helix; polyproline II (PPII) helix; helical wheel; wire diagrams; protein secondary structure |
Department/Centre: | Division of Biological Sciences > Molecular Biophysics Unit |
Date Deposited: | 15 Jun 2015 05:23 |
Last Modified: | 15 Jun 2015 05:23 |
URI: | http://eprints.iisc.ac.in/id/eprint/51642 |
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