Services three-dimensional protein structures

The World Wide Web site of the Protein Data Bank at the RCSB offers a number of services for submitting and retrieving three-dimensional structure data. The home page of the RCSB site provides links to services for depositing three-dimensional structures, information on how to obtain the status of structures undergoing processing for submission, ways to download the PDB database, and links to other relevant sites and software. 

Links. PDB s search engine, the Structme Explorer, can be used to retrieve PDB records, as shown in Figure 5.2. The Structure Explorer is also the primary database of links to third-party aimotation of PDB structure data. There are a number of links maintained in the Structure Explorer to Internet-based three-dimensional structure services on other Web sites. Figme 5.2 shows the Structure Summary for the protein bamase (IBNR Bycroft et al., 1991). The Structure Explorer also provides links to special project databases maintained by researchers interested in related topics, such as structural evolution (FSSP Holm and Sander, 1993), structure-structure similarity (DALI Holm and Sander, 1996), and protein motions (Gerstein et al., 1994). Links to visualization tool-ready versions of the structure are provided, as well as authored two-dimensional images that can be very helpful to see how to orient a three-dimensional structure for best viewing of certain features such as binding sites. 

Protein Sequences That Fold Into a Known Three-Dimensional Structure. The Verify3D server http //www.doe-mbl.ucla.edu/Services/Verify 3D/. 

The Protein Data Bank (PDB) at Brookhaven National Laboratory is a database containing experimentally determined, three-dimensional structures of proteins, nucleic acids, and other biological macromolecules. The PDB has a history of service starting in 1971 to a global community of researchers, educators, and students in a variety of scientific disciplines. The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data. Scientists around the world contribute structures to the PDB and use it on a daily basis. The common interest shared by this community is a need to access information that can relate the biological functions of macromolecules to their three-dimensional structures. 

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