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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	http://www.rcsb.org/pdb; 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	http://www.ncbi.nlm.nih.gov/Structure/
Structural Classification of Proteins at Cambridge University	SCOP database of structural relationships among known protein structures classified by superfamily, family, and fold	http://scop.mrc-lmb.cam.ac.uk/scop; 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	http://www.biochem.ucl.ac.uk/bsm; also at Web mirror sites
European Bioinformatics Institute, Hinxton, Cambridge	Databases, TOPS protein structural topology cartoons, Dali domain server, and FSSP databaseb	http://www.tops.leeds.ac.uk/
The PredictProtein server at the European Molecular Biology Laboratory at Heidelberg, Germany	Important site for secondary structure prediction by PHD, PREDATOR, TOPITS, threader	http://cubic.bioc.columbia.edu/predictprotein; 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	http://www.expasy.ch/
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 http://www.expasy.ch/swissmod/course/course-index.htm. There is also a Web course in protein structure at Birkbeck College http://www.cryst.bbk.ac.uk/teaching/.     a A summary of the PDB entries is provided at http://www.biochem.ucl.ac.uk/bsm/pdbsum/ (Laskowski et al. 1997).     b 3Dee database of protein domains at http://barton.ebi.ac.uk/servers/3Dee.html. Dali domain server is at http://www2.embl-ebi.ac.uk/dali/domain/ and FSSP database at http://www2.embl-ebi.ac.uk/dali/fssp/fssp.html.     c Also performed at the structure prediction server at http://fold.doe-mbi.ucla.edu/.     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.