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Nucleic Acids Research Advance Access originally published online on April 7, 2009
Nucleic Acids Research 2009 37(11):3522-3530; doi:10.1093/nar/gkp212
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Nucleic Acids Research, 2009, Vol. 37, No. 11 3522-3530
© 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.

Computational Biology

PROCAIN: protein profile comparison with assisting information

Yong Wang1, Ruslan I. Sadreyev2 and Nick V. Grishin2,3,*

1Biomedical Engineering Program, University of Texas Southwestern Medical Center, 2Howard Hughes Medical Institute and 3Department of Biochemistry, University of Texas Southwestern Medical Center Dallas, TX 75390-9050, USA

*To whom correspondence should be addressed. Email: grishin{at}chop.swmed.edu

Received March 2, 2009. Revised March 12, 2009. Accepted March 16, 2009.

Detection of remote sequence homology is essential for the accurate inference of protein structure, function and evolution. The most sensitive detection methods involve the comparison of evolutionary patterns reflected in multiple sequence alignments (MSAs) of protein families. We present PROCAIN, a new method for MSA comparison based on the combination of ‘vertical’ MSA context (substitution constraints at individual sequence positions) and ‘horizontal’ context (patterns of residue content at multiple positions). Based on a simple and tractable profile methodology and primitive measures for the similarity of horizontal MSA patterns, the method achieves the quality of homology detection comparable to a more complex advanced method employing hidden Markov models (HMMs) and secondary structure (SS) prediction. Adding SS information further improves PROCAIN performance beyond the capabilities of current state-of-the-art tools. The potential value of the method for structure/function predictions is illustrated by the detection of subtle homology between evolutionary distant yet structurally similar protein domains. ProCAIn, relevant databases and tools can be downloaded from: http://prodata.swmed.edu/procain/download. The web server can be accessed at http://prodata.swmed.edu/procain/procain.php.


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Y. Wang, R. I. Sadreyev, and N. V. Grishin
PROCAIN server for remote protein sequence similarity search
Bioinformatics, August 15, 2009; 25(16): 2076 - 2077.
[Abstract] [Full Text] [PDF]


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