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Nucleic Acids Research Advance Access originally published online on May 25, 2007
Nucleic Acids Research 2007 35(Web Server issue):W357-W362; doi:10.1093/nar/gkm231
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W357-W362
© 2007 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

PI2PE: protein interface/interior prediction engine

Harianto Tjong, Sanbo Qin and Huan-Xiang Zhou*

Institute of Molecular Biophysics and School of Computational Science and Department of Physics, Florida State University, Tallahassee, FL 32306, USA

*To whom correspondence should be addressed. Tel: +1 850 645 1336; Fax: +1 850 644 7244; Email: zhou{at}sb.fsu.edu

Received January 17, 2007. Revised March 8, 2007. Accepted March 29, 2007.

The side chains of the 20 types of amino acids, owing to a large extent to their different physical properties, have characteristic distributions in interior/surface regions of individual proteins and in interface/non-interface portions of protein surfaces that bind proteins or nucleic acids. These distributions have important structural and functional implications. We have developed accurate methods for predicting the solvent accessibility of amino acids from a protein sequence and for predicting interface residues from the structure of a protein-binding or DNA-binding protein. The methods are called WESA, cons-PPISP and DISPLAR, respectively. The web servers of these methods are now available at http://pipe.scs.fsu.edu. To illustrate the utility of these web servers, cons-PPISP and DISPLAR predictions are used to construct a structural model for a multicomponent protein–DNA complex.


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S. Qin and H.-X. Zhou
meta-PPISP: a meta web server for protein-protein interaction site prediction
Bioinformatics, December 15, 2007; 23(24): 3386 - 3387.
[Abstract] [Full Text] [PDF]


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