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PROMALS3D: Multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information

Jimin Pei; Nick V. Grishin

(Profiled Author: Nick V Grishin)

Methods in Molecular Biology. 2014;1079:263-271.

Abstract

Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D. © 2014 Springer Science+Business Media, LLC.


PMID: 24170408    

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