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

Jimin Pei, Nick V. Grishin

Research output: Chapter in Book/Report/Conference proceedingChapter

115 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages263-271
Number of pages9
Volume1079
ISBN (Print)9781627036450
DOIs
StatePublished - 2014

Publication series

NameMethods in Molecular Biology
Volume1079
ISSN (Print)10643745

Keywords

  • Consistency-based scoring
  • Database searches
  • Multiple sequence alignment
  • Probabilistic model of profile-profile alignment
  • Three-dimensional structural alignment

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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    Pei, J., & Grishin, N. V. (2014). PROMALS3D: Multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. In Methods in Molecular Biology (Vol. 1079, pp. 263-271). (Methods in Molecular Biology; Vol. 1079). Humana Press Inc.. https://doi.org/10.1007/978-1-62703-646-7_17