Identification of local variations within secondary structures of proteins

Kumar, Prasun ; Bansal, Manju (2015) Identification of local variations within secondary structures of proteins Acta Crystallographica Section D Biological Crystallography, 71 (5). pp. 1077-1086. ISSN 1399-0047

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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 Cα 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 α-helices, 310-helices, π-helices, extended β-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 α-helices and extended β-strands, 310-helices and π-helices were also found to occur in substantial numbers. ASSP was able to discriminate non-α-helical segments from flanking α-helices, which were often identified as part of α-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.

Item Type:Article
Source:Copyright of this article belongs to International Union of Crystallography.
Keywords:ASSP; π-Helix; Polyproline II (PPII) Helix; Helical Wheel; Wire Diagrams; Protein Secondary Structure
ID Code:112107
Deposited On:31 Jan 2018 04:09
Last Modified:31 Jan 2018 04:09

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