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Nucleic Acids Research Advance Access originally published online on February 20, 2008
Nucleic Acids Research 2008 36(7):2295-2300; doi:10.1093/nar/gkn072
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Nucleic Acids Research, 2008, Vol. 36, No. 7 2295-2300
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

PROMALS3D: a tool for multiple protein sequence and structure alignments

Jimin Pei1,*, Bong-Hyun Kim2 and Nick V. Grishin1,2

1Howard Hughes Medical Institute and 2Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA

*To whom correspondence should be addressed. Tel: +214 645 5951; Fax: +214 645 5948; Email: jpei{at}chop.swmed.edu

Received November 29, 2007. Revised January 30, 2008. Accepted February 5, 2008.

Although multiple sequence alignments (MSAs) are essential for a wide range of applications from structure modeling to prediction of functional sites, construction of accurate MSAs for distantly related proteins remains a largely unsolved problem. The rapidly increasing database of spatial structures is a valuable source to improve alignment quality. We explore the use of 3D structural information to guide sequence alignments constructed by our MSA program PROMALS. The resulting tool, PROMALS3D, automatically identifies homologs with known 3D structures for the input sequences, derives structural constraints through structure-based alignments and combines them with sequence constraints to construct consistency-based multiple sequence alignments. The output is a consensus alignment that brings together sequence and structural information about input proteins and their homologs. PROMALS3D can also align sequences of multiple input structures, with the output representing a multiple structure-based alignment refined in combination with sequence constraints. The advantage of PROMALS3D is that it gives researchers an easy way to produce high-quality alignments consistent with both sequences and structures of proteins. PROMALS3D outperforms a number of existing methods for constructing multiple sequence or structural alignments using both reference-dependent and reference-independent evaluation methods.


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J. Pei, M. Tang, and N. V. Grishin
PROMALS3D web server for accurate multiple protein sequence and structure alignments
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W30 - W34.
[Abstract] [Full Text] [PDF]


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