Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling.

ABSTRACT:

Motivation

Building an accurate alignment of a large set of distantly related protein structures is still very challenging.

Results

This article presents a novel method 3DCOMB that can generate a multiple structure alignment (MSA) with not only as many conserved cores as possible, but also high-quality pairwise alignments. 3DCOMB is unique in that it makes use of both local and global structure environments, combined by a statistical learning method, to accurately identify highly similar fragment blocks (HSFBs) among all proteins to be aligned. By extending the alignments of these HSFBs, 3DCOMB can quickly generate an accurate MSA without using progressive alignment. 3DCOMB significantly excels others in aligning distantly related proteins. 3DCOMB can also generate correct a

SUBMITTER: Wang S 

PROVIDER: S-EPMC3167051 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature