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Nucleic Acids Research Advance Access first published online on May 30, 2007
This version published online on June 1, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm401
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© 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.

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Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces

Shula Shazman1, Gershon Celniker1, Omer Haber1, Fabian Glaser2 and Yael Mandel-Gutfreund1,*

1Department of Biology and 2The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology Haifa 32000, Israel

*To whom correspondence should be addressed. Tel: 972 4 8293958; Fax: 972 4 8225153; Email: yaelmg{at}tx.technion.ac.il

Received February 15, 2007. Revised April 30, 2007. Accepted May 1, 2007.

Positively charged electrostatic patches on protein surfaces are usually indicative of nucleic acid binding interfaces. Interestingly, many proteins which are not involved in nucleic acid binding possess large positive patches on their surface as well. In some cases, the positive patches on the protein are related to other functional properties of the protein family. PatchFinderPlus (PFplus) http://pfp.technion.ac.il is a web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces. The input required for PFplus is either a four letter PDB code or a protein coordinate file in PDB format, provided by the user. PFplus computes the continuum electrostatics potential and extracts the largest positive patch for each protein chain in the PDB file. The server provides an output file in PDB format including a list of the patch residues. In addition, the largest positive patch is displayed on the server by a graphical viewer (Jmol), using a simple color coding.


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