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

J-C Gelly; C Etchebest; S Hazout; A G de Brevern

doi:10.1093/nar/gkl292

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

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W75-8. doi: 10.1093/nar/gkl292.

Authors

J-C Gelly¹, C Etchebest, S Hazout, A G de Brevern

Affiliation

¹ CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie, Physico-Chimique (FRC 550) 11, rue Pierre et Marie Curie, 75005 Paris, France.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computer Graphics
Internet
Protein Conformation*
Protein Folding
Proteins / chemistry
Software*
User-Computer Interface

Substances

Proteins