STRUCTURAL DATABASES OF BIOMOLECULES, THE PDB AND NDB

Bohdan Schneider

Institute of Biotechnology, Czech Academy of Sciences, Videnska 1083, CZ-142 20 Prague, Czech Republic

The Protein Data Bank, PDB [1] (http://www.pdb.org/), is the main publically accessible resource for structural biology and the central archive for biomolecular three-dimensional structures determined experimentally by x-ray crystallography, NMR techniques, electron (cryo)microscopy, and neutron diffraction. It is jointly operated by the Worldwide Protein Data Bank (wwPDB, http://www.wwpdb.org/). The main website (http://www.rcsb.org) offers several main services: deposition of new structures, search of the archive, analysis of structures, and others. The PDB has developed many tools for the deposition and validation of structures, all easily available from the web, and serves as the main hub for deposition, data processing and distribution of the biomolecules. The archive can be queried. The queried structures can be downloaded in the historical PDB format or in mmCIF format [2], individually inspected (“browsed”), and their user-selected properties arranged into tabular reports. The archive contains both coordinates and “experimental” files of the deposited structures (structure factors for x-ray, distance constraint files for NMR structures).

The talk will give an overview of the archive, introduce some basic features of the website, suggest effective ways how to query the archive, and how to create an useful report of the queried structures.

Nucleic Acid Database, NDB [3] (http://ndbserver.rutgers.edu) was established in 1991 as a resource for experts on nucleic acid structures. It contains both X-ray and NMR structures containing dinucleotide and longer sequences. The core of the NDB is its relational database of primary and derivative data specifically related to structure of nucleic acids. The database offers rich query and reporting capabilities. We will briefly show specific features of NDB.

Data distribution. Coordinate files, database reports, software, and other resources are freely available from the web pages of both databases.

This study was supported by BIOCEV CZ.1.05/1.1.00/ 02.0109 from the ERDF and by institutional grant to Institute of Biotechnology, CAS (RVO: 86 652 036).

 

[1] Berman H.M., Battistuz T., Bhat T.N., Bluhm W.F., Bourne P.E., Burkhardt K., Feng Z., Gilliland G.L., Iype L., Jain S., Fagan P., Marvin J., Padilla D., Ravichandran V., Schneider B., Thanki N., Weissig H., Westbrook J.D., Zardecki, C. (2002): The Protein Data Bank. Acta Crystallogr D, 58, 899-907.

[2] Bourne P.E., Berman H.M., Watenpaugh K., Westbrook J.D., Fitzgerald P.M.D. (1997): The macromolecular crystallographic information file (mmCIF). Methods Enzymol. 277, 571–590.

[3] Berman H.M., Olson W.K., Beveridge D.L., Westbrook J., Gelbin A., Demeny T., Hsieh S.-H., Srinivasan A.R., Schneider B. (1992): The Nucleic Acid Database—a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63,751–759.