title: PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.
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.
authors.affiliation: Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
authors.forename: Jimin
authors.initials: J
authors.lastname: Pei
authors.forename: Nick V
authors.initials: NV
authors.lastname: Grishin
mesh_terms: D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D020407:Internet; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins