Retrieving backbone string neighbors provides insights into structural modeling of membrane proteins.

ABSTRACT: Identification of protein structural neighbors to a query is fundamental in structure and function prediction. Here we present BS-align, a systematic method to retrieve backbone string neighbors from primary sequences as templates for protein modeling. The backbone conformation of a protein is represented by the backbone string, as defined in Ramachandran space. The backbone string of a query can be accurately predicted by two innovative technologies: a knowledge-driven sequence alignment and encoding of a backbone string element profile. Then, the predicted backbone string is employed to align against a backbone string database and retrieve a set of backbone string neighbors. The backbone string neighbors were shown to be close to native structures of query proteins. BS-align was successf

SUBMITTER: Sun JM 

PROVIDER: S-EPMC3394956 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature