Multiple Sequence Alignment Methods pp 263-271

Part of the Methods in Molecular Biology book series (MIMB, volume 1079) | Cite as

PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and Three-Dimensional Structural Information

  • Jimin Pei
  • Nick V. Grishin


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

Key words

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


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Copyright information

© Springer Science+Business Media, LLC 2014

Authors and Affiliations

  • Jimin Pei
    • 1
  • Nick V. Grishin
    • 2
    • 3
  1. 1.Howard Hughes Medical InstituteUniversity of Texas Southwestern Medical CenterDallasUSA
  2. 2.Department of BiophysicsHoward Hughes Medical InstituteDallasUSA
  3. 3.Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasUSA

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