Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment.

ABSTRACT:

Background

The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult.

Results

We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular

SUBMITTER: Daniels NM 

PROVIDER: S-EPMC3585936 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature