Abstract

Protein Data Bank - reaching out to our users

Biology Department, Brookhaven National Laboratory, Upton, NY, 11973-5000 USA
Dept. of Structural Biology and Bioinformatics Unit, Weizmann Institute of Science, 76100 Rehovot, ISRAEL

oeder@pdb.pdb.bnl.gov

The Protein Data Bank (PDB) is an archive of experimentally-determined three-dimensional structures of biological macromolecules. In order to better serve our global community of researchers, educators, and students, the PDB has expanded our user services over the past year.

- AutoDep -
The new World Wide Web-based graphical user interface (AutoDep), which streamlines the deposition procedure, is now available. AutoDep reduces the time needed to fill out the deposition form and increases the accuracy and information content of a PDB entry. AutoDep may be initialized with data from any released PDB entry or from one of the depositor's previous submissions. Additionally, PDB-formatted output from refinement programs may be merged into the submission form. The resultant bibliographic portion of the PDB entry may be previewed at any time in order to check progress.

The completed AutoDep submission is passed through a syntax checker and then PDB's validation procedure, which includes stereochemical and geometry checks (WhatCheck by G. Vriend and R. Hooft, verification routines from WHAT IF; ProCheck by R.A. Laskowski, et al.). Output diagnostics are returned along with the PDB ID code within minutes of submission. All entries are then reviewed by PDB staff for consistency of representation and quality control.

- Contents Guide -
The new PDB Contents Guide, which details the exact format of atomic coordinate entries, was released earlier this year. Crucial in the effort to produce CIF-compliant data files from PDB entries, this document served as the foundation of AutoDep. All entries released after April 15, 1996 comply with this format.

- World Wide Web -
PDB's World Wide Web site (http://www.pdb.bnl.gov) is always evolving to better serve our users. The Web Home Page presents the current number of released entries, a dynamically chosen image of a molecule in the database, access to the latest PDB Newsletter, and links to the sub-pages summarized below:

• Searching and Browsing the PDB - PDB's new 3DB Browser, a search of the pending/on hold entry list, a list of all sequences in the PDB in FASTA format, and the Het Group Dictionary.
• Submitting Data to the PDB - gateway to AutoDep, submission forms and policies.
• PDB FTP Server - an indexed view of the PDB FTP server.
• PDB Documentation - The PDB Contents Guide, PDB Newsletter archives, statistics, and order forms.
• PDB Mirror Sites - links to each of the four official PDB Mirror Sites throughout the world. At least seven more will be on-line soon.
• PDB Users Group - representing the diverse spectrum of users.
• mmCIF - Macromolecular Crystallographic Information File
• Molecular Biology Servers/Databases/Web Sites of Interest - a growing list of related Web sites.
• Software and Related Information - programs being distributed by PDB, as well as links to some program-related Web sites.

- Database -
The PDB is easily queried by the new 3DB Browser, which allows full text queries of the database while imposing various constraints. Returned entries may be viewed with or without coordinates, in PDB or mmCIF format, or graphically. There are links to many related resources and user-supplied annotations.

- Newsletter -
PDB's Quarterly Newsletter now contains articles contributed by top researchers and program developers from around the world. Available both on-line and through postal distribution, the Newsletter reaches thousands of readers. The archives are also distributed quarterly on CD-ROMs.

- Help Desk -
PDB has also established a Help Desk, reachable by phone at 516-344-6356 and by e-mail at pdbhelp@bnl.gov. The Help Desk responds quickly to users' questions and problems.

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 and user fees.

References:
1. Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F., and Weng, J. Protein Data Bank, in Crystallographic Databases - Information Content, Software Systems, Scientific Applications, F.H. Allen, G. Bergerhoff, and R. Sievers, eds., Data Commission of the International Union of Crystallography, Bonn/Cambridge/Chester, 107-132, 1987.
2. Vriend, G. WHAT IF: A molecular modeling and drug design program. J. Mol. Graph. 8, 52-56, 1990.
3. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 26, 283-291, 1993.