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Table 10.1. Main Web sites for protein structural analysis
Name of resource   Resources available   Internet address
Protein data bank (PDB) at the State University of New Jersey (Rutgers)a Atomic coordinates of structures as PDB files, models, viewers, links to many other Web sites for structural analysis and classification;
also at mirror Web sites (Berman et al. 2000)
National Center for Biotechnology Information Structure Group Molecular Modelling Database (MMDB), Vector Alignment Search Tool (VAST) for structural comparisons, viewers, threader software
Structural Classification of Proteins at Cambridge University SCOP database of structural relationships among known protein structures classified by superfamily, family, and fold;
also at Web mirror sites
Biomolecular Structure and Modelling group at the University College, London CATH database, a hierarchical domain classification of protein structures by class, architecture, fold family and superfamily, other databases and structural analyses, threader software;
also at Web mirror sites
European Bioinformatics Institute, Hinxton, Cambridge Databases, TOPS protein structural topology cartoons, Dali domain server, and FSSP databaseb
The PredictProtein server at the European Molecular Biology Laboratory at Heidelberg, Germany Important site for secondary structure prediction by PHD, PREDATOR, TOPITS, threader;
also at Web mirror sitesc
Swiss Institute of Bioinformatics, Geneva Basic types of protein analysisd databases, the Swiss-Model resource for prediction of protein models, Swiss-PdbViewer
    Additional sites are listed in the text. In addition to these sites, there are a number of Web sites and courses that discuss protein structure. The Swiss Institute for Bioinformatics (ISREC server) provides a tutorial on Principles of Protein Structure, Comparative Protein Modelling, and Visualisation at There is also a Web course in protein structure at Birkbeck College
    a A summary of the PDB entries is provided at (Laskowski et al. 1997).
    b 3Dee database of protein domains at Dali domain server is at and FSSP database at
    c Also performed at the structure prediction server at
    d This site offers a series of basic types of protein analyses to assist with protein identification, including identification by amino acid composition, charge, size, and sequence fingerprint. Predictions of posttranslational modifications and oligosaccharide structures are also available.


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