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Nucleic Acids Research Advance Access originally published online on May 12, 2009
Nucleic Acids Research 2009 37(Web Server issue):W90-W94; doi:10.1093/nar/gkp360
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W90-W94
© 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

COMPASS server for homology detection: improved statistical accuracy, speed and functionality

Ruslan I. Sadreyev1,*, Ming Tang1, 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 75390-9050, USA

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

Received March 10, 2009. Revised April 23, 2009. Accepted April 23, 2009.

COMPASS is a profile-based method for the detection of remote sequence similarity and the prediction of protein structure. Here we describe a recently improved public web server of COMPASS, http://prodata.swmed.edu/compass. The server features three major developments: (i) improved statistical accuracy; (ii) increased speed from parallel implementation; and (iii) new functional features facilitating structure prediction. These features include visualization tools that allow the user to quickly and effectively analyze specific local structural region predictions suggested by COMPASS alignments. As an application example, we describe the structural, evolutionary and functional analysis of a protein with unknown function that served as a target in the recent CASP8 (Critical Assessment of Techniques for Protein Structure Prediction round 8). URL: http://prodata.swmed.edu/compass


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