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Nucleic Acids Research 2004 32(Web Server Issue):W50-W54; doi:10.1093/nar/gkh456
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

Consensus alignment server for reliable comparative modeling with distant templates

Jahnavi C. Prasad1, Sandor Vajda2 and Carlos J. Camacho1,2,*

1 Bioinformatics Graduate Program and 2 Biomedical Engineering, Boston University, Boston, MA 02215, USA

* To whom correspondence should be addressed. Tel: +1 617 353 4842; Fax: +1 617 353 6766; Email: ccamacho{at}bu.edu

Received February 15, 2004; Revised March 19, 2004; Accepted April 26, 2004

Consensus is a server developed to produce high-quality alignments for comparative modeling, and to identify the alignment regions reliable for copying from a given template. This is accomplished even when target–template sequence identity is as low as 5%. Combining the output from five different alignment methods, the server produces a consensus alignment, with a reliability measure indicated for each position and a prediction of the regions suitable for modeling. Models built using the server predictions are typically within 3 Å rms deviations from the crystal structure. Users can upload a target protein sequence and specify a template (PDB code); if no template is given, the server will search for one. The method has been validated on a large set of homologous protein structure pairs. The Consensus server should prove useful for modelers for whom the structural reliability of the model is critical in their applications. It is currently available at http://structure.bu.edu/cgi-bin/consensus/consensus.cgi.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.


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