3DBASE - A MACROMOLECULAR STRUCTURE DATABASE. E.E.Abola, J.Prilusky, N.O.Manning, J.L.Sussman, Chemistry Department, Brookhaven National Laboratory, P.O. Box 5000, Upton, NY, 11973-5000 USA and Bioinformatics Unit, Weizmann Institute of Science, 76100 Rehovot, Israel

The Protein Data Bank (PDB) is an archive of experimentally- determined three-dimensional structures of biological macromolecules. We will describe the new relational database, 3DBase, that represents the structural, biological, chemical, and bibliographic information found in the PDB archives.

3DBase is constructed with the SYBASE DBMS and the Object Protocol Model (OPM) and OPM data management tools developed by Victor Markowitz's group at Lawrence Berkeley National Laboratory. SYBASE provides a powerful and robust environment for data management, the OPM tools allow rapid development of SYBASE databases, while OPM's object-oriented view provides a scientifically intuitive representation of data.

Objects have been incorporated into the database schema that allow for description and access of 3-dimensional information from a number of viewpoints. Crystallographers can access a full description of the diffraction study via the oExperiment Object, while structural data on the biologically active molecule are accessed through oMacromolecule. 3DBase also includes facilities for extended annotation by outside users of any accessible object.

Access to 3DBase is provided primarily through a Web browser constructed using the Genera software package developed by Stan Letovsky of Johns Hopkins Medical Institutes. In addition to accessing data stored in 3DBase, the browser provides links to entries in other databases. Graphical views of molecules are provided in the browser by use of Roger Sayle's Rasmol program along with graphical annotation commands stored in the database. In the future, multiple interfaces to 3DBase will be provided with support for queries of increased complexity.

The PDB is supported by a combination of Federal Government Agency funds and user fees. Support is provided by the U.S. National Science Foundation, the U.S. Public Health Service, National Institutes of Health, National Center for Research Resources, National Institutes of General Medical Sciences, National Library of Medicine, and the U.S. Department of Energy under contract DE-AC02-76CH00016.