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Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W30-4. doi: 10.1093/nar/gkn322. Epub 2008 May 24.

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

Author information

1
Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9050, USA.

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/.

PMID:
18503087
PMCID:
PMC2447800
DOI:
10.1093/nar/gkn322
[Indexed for MEDLINE]
Free PMC Article

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