CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations

Sandhya, Sankaran and Pankaj, Barah and Govind, Madabosse Kande and Offmann, Bernard and Srinivasan, Narayanaswamy and Sowdhamini, Ramanathan (2008) CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. In: BMC Structural Biology, 8 (28).

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Abstract

Distantly related proteins adopt and retain similar structural scaffolds despite length variations that could be as much as two-fold in some protein superfamilies. In this paper, we describe an analysis of indel regions that accommodate length variations amongst related proteins. We have developed an algorithm CUSP, to examine multi-membered PASS2 superfamily alignments to identify indel regions in an automated manner. Further, we have used the method to characterize the length, structural type and biochemical features of indels in related protein domains.

Item Type:	Journal Article
Publication:	BMC Structural Biology
Publisher:	BioMed Central
Additional Information:	Copyright of this article belongs to BioMed Central.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	15 Jul 2008
Last Modified:	19 Sep 2010 04:47
URI:	http://eprints.iisc.ac.in/id/eprint/14956

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