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

Methods Mol Biol. 2014;1079:263-71. doi: 10.1007/978-1-62703-646-7_17.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Evolution, Molecular*
  • Internet
  • Protein Conformation
  • Proteins / chemistry*
  • Sequence Alignment / methods*
  • Software*

Substances

  • Proteins