Proteomic servers

Gasteiger, E. Gattiker, A. Hoogland, C. Ivanyi, I. Appel, R. D. Bairoch, A. ExPASy The proteomics server for in-depth protein knowledge and analysis. Nucl. Acids Res. 2003,31, 3784-3788. 

Proteomics server of the Swiss institute of bioinformatics. Dedicated to analysis of protein sequences and structure, as well as 2-D SDS-PAGE. 

The ExPASy (Expert Protein Analysis System, http //www.expasy.ch/) proteomics server of the Swiss Institute of Bioinformatics, P05790. 

As explained above (Sect. 7.3), our unfolded state model is very simple. To obtain native-like sequences in the redesigned proteins, an empirical correction is added to the energy function, such that the overall amino acid composition of the computed sequences matches the experimental composition for this class of proteins. We obtained the experimental amino acid composition from the ExPASy Proteomics Server, which is available free of charge via the Internet. Only protein sequences that share a minimum of 35 % sequence identity with the target structures were considered. Computed sequences were obtained with certain amino acid types frozen in their native type alanines, cysteines, prolines and glycines were not mutated, because these amino acids have a particular, strong effect on the local backbone... 

In this Section, we describe a number of protein identification and characterisation tools available on the World-Wide Web (WWW). All the tools described here are accessible from the ExPASy tools page http //www. expasy.org/tools/, which is constantly updated. Particular emphasis will be given to the programs provided on the ExPASy proteomics server [23, http //www.expasy.org]. Note that currently the Geneva ExPASy server (www. 

The CMS Molecular Biology Resource [168] at the San Diego Supercomputer Center contains an excellent compendium of Web-accessible bioinformatics tools. The ExPASy (Expert Protein Analysis System] proteomics server of the Swiss Institute of Bioinformatics [169] and the EBI Toolbox are two other popular tool collections. Another useful resource is Herbert Mayer s Bioinformatics World Web site, which contains a comprehensive collection of bioinformatics tools and software, including evaluations, comments, and tutorials. 

The ExPASy Proteomic Server (http //www.expasy.org) or its mirror site (e.g. http //us.expasy.org in U.S.A. and http //ca.expay.org in Canada) provides comprehensive resources and tools for proteomic analyses. They include Databases (e.g. Swiss-Prot, Prosite, Enzyme), Tools (e.g. BLAST, ProtParam, ProtScale, SIM, SWISS-MODEL, Translate), Services (e.g. ExPASy ftp server, BioHunt, 2D Hunt), Documentation and links. 

Res., 31, 3784 (2003). ExPASy The Proteomics Server for In-depth Protein Knowledge and Analysis. The ExPASy website www.expasy.org. 

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