PROMALS3D web server for accurate multiple protein sequence and structure alignments.

Jimin Pei, Ming Tang, Nick V. Grishin

Research output: Contribution to journalArticle

92 Citations (Scopus)

Abstract

Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume36
Issue numberWeb Server issue
DOIs
StatePublished - Jul 1 2008

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Sequence Alignment
Databases
Proteins
Consensus Sequence
Sequence Analysis

ASJC Scopus subject areas

  • Genetics

Cite this

PROMALS3D web server for accurate multiple protein sequence and structure alignments. / Pei, Jimin; Tang, Ming; Grishin, Nick V.

In: Nucleic Acids Research, Vol. 36, No. Web Server issue, 01.07.2008.

Research output: Contribution to journalArticle

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