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BMCBI
2011

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

10 years 3 months ago
Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs
Background: One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results: Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with kn...
Leslie Regad, Juliette Martin, Anne-Claude Camprou
Added 24 Aug 2011
Updated 24 Aug 2011
Type Journal
Year 2011
Where BMCBI
Authors Leslie Regad, Juliette Martin, Anne-Claude Camproux
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