A comprehensive analysis of non-sequential alignments between all protein structures.

ABSTRACT:

Background

The majority of relations between proteins can be represented as a conventional sequential alignment. Nevertheless, unusual non-sequential alignments with different connectivity of the aligned fragments in compared proteins have been reported by many researchers. It is interesting to understand those non-sequential alignments; are they unique, sporadic cases or they occur frequently; do they belong to a few specific folds or spread among many different folds, as a common feature of protein structure. We present here a comprehensive large-scale study of non-sequential alignments between available protein structures in Protein Data Bank.

Results

The study has been conducted on a non-redundant set of 8,865 protein structures aligned with the aid of the TOPOFIT method

SUBMITTER: Abyzov A 

PROVIDER: S-EPMC2213659 | biostudies-literature | 2007 Nov

REPOSITORIES: biostudies-literature