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Nucleic Acids Research 2006 34(Web Server issue):W75-W78; doi:10.1093/nar/gkl292
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

Protein Peeling 2: a web server to convert protein structures into series of protein units

J.-C. Gelly, C. Etchebest1, S. Hazout1,{dagger} and A.G. de Brevern1,*

CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie, Physico-Chimique (FRC 550) 11, rue Pierre et Marie Curie, 75005 Paris, France 1 INSERM, U726, Equipe de Bioinformatique Génomique et Moléculaire (EBGM) Université Paris 7, case 7113, 2, place Jussieu, 75251 Paris Cedex 05, France

*To whom correspondence should be addressed. Tel: +33 1 44 27 77 31; Fax: +33 1 43 26 38 30; Email: debrevern{at}ebgm.jussieu.fr

Received February 12, 2006. Revised April 1, 2006. Accepted April 6, 2006.

Protein Peeling 2 (PP2) is a web server for the automatic identification of protein units (PUs) given the 3D coordinates of a protein. PUs are an intermediate level of protein structure description between protein domains and secondary structures. It is a new tool to better understand and analyze the organization of protein structures. PP2 uses only the matrices of protein contact probabilities and cuts the protein structures optimally using Matthews' coefficient correlation. An index assesses the compactness quality of each PU. Results are given both textually and graphically using JMol and PyMol softwares. The server can be accessed from http://www.ebgm.jussieu.fr/~gelly/index.html.

{dagger}Deceased author.


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