Using the World Wide Web - a Guide For Graduate Students

The World Wide Web and Protein Science

Structural

Some important and interesting examples:

The Brookhaven Protein Databank can be easily searched and structures downloaded if necessary, including the Pending/Waiting List and On Hold List.
The Structural Classification of Proteins (SCOP) database at the MRC Laboratory of Molecular Biology and Centre for Protein Engineering.
The "Class, Architecture, Topology, Homology" (CATH) protein classification database at UCL.
Swiss-3DImage, a database of a fairly large selection of PDB structures is maintained by Manuel Peitsch at ExPASy.
You can also produce your own images of PDB files to order using the Web, with Molviewer at York.
The Protein Motions Database at Stanford.

The beauty of it is that easy access can be provided to cross-references in either databases and resources; e.g. SCOP has hypertext links to Swiss-3DImage, Entrez Sequence Entries, Brookhaven, Protein Motions Database, and others.

A list of some structural databases

Sequences

A nice introduction to Protein Sequence Motifs is provided by Emer Brizzolara's project for the "virtual" course in The Principles of Protein Structure run from this department earlier this year.
An excellent and comprehenseive step-by-step tutorial on Bioinformatics and the Web from Terri Attwood at UCL.

Links to some sequence databases

Some particularly useful general lists:

Ethan Benatan's and Cornelius Krasel's Protein-Structure Related Databases
Pedro Mendes' BioMolecular Research Tools

And theres the department's Springboard to the World.

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