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

ABSTRACT:

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

SUBMITTER: Regad L 

PROVIDER: S-EPMC3158783 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature