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Nucleic Acids Research Advance Access originally published online on May 5, 2009
Nucleic Acids Research 2009 37(Web Server issue):W532-W538; doi:10.1093/nar/gkp328
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W532-W538
© 2009 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.

Articles

HorA web server to infer homology between proteins using sequence and structural similarity

Bong-Hyun Kim1, Hua Cheng1,2 and Nick V. Grishin1,2,*

1Department of Biochemistry and 2Howard Hughes Medical Institute and University of Texas, Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA

*To whom correspondence should be addressed. Tel: +214-645-5952; Fax: +214-645-5948; Email: grishin{at}chop.swmed.edu

Received February 15, 2009. Revised April 9, 2009. Accepted April 20, 2009.

The biological properties of proteins are often gleaned through comparative analysis of evolutionary relatives. Although protein structure similarity search methods detect more distant homologs than purely sequence-based methods, structural resemblance can result from either homology (common ancestry) or analogy (similarity without common ancestry). While many existing web servers detect structural neighbors, they do not explicitly address the question of homology versus analogy. Here, we present a web server named HorA (Homology or Analogy) that identifies likely homologs for a query protein structure. Unlike other servers, HorA combines sequence information from state-of-the-art profile methods with structure information from spatial similarity measures using an advanced computational technique. HorA aims to identify biologically meaningful connections rather than purely 3D-geometric similarities. The HorA method finds ~90% of remote homologs defined in the manually curated database SCOP. HorA will be especially useful for finding remote homologs that might be overlooked by other sequence or structural similarity search servers. The HorA server is available at http://prodata.swmed.edu/horaserver.


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