CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.

ABSTRACT:

Motivation

Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information.

Method

We present a novel network-based protein homology detection method, CMsearch, b

SUBMITTER: Cui X 

PROVIDER: S-EPMC4908355 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature