From owner-biophysics@net.bio.net Thu Sep 23 21:09:00 1999
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From: DMCGAVIN@biophysics.faseb.org
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Subject: The New Protein DataBank
Date: 23 Sep 1999 15:09:47 -0700
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On July 1, 1999, the Research Collaboratory for Structural Bioinformatics
(RCSB) became fully responsible for the operation of the Protein Data Bank
(PDB). Throughout the nine-month transition period, which began when the
National Science Foundation announced the award on October 1, 1998, a
concentrated effort was made to ensure that the transition of management
between Brookhaven National Laboratory (BNL) and the RCSB was as seamless
and non-disruptive as possible.  Users who went to the PDB site on June
30,
1999, were automatically redirected to the new home of the PDB at
http://www.rcsb.org/ 

During the transition period, the RCSB phased in many new features of the
PDB. A Web-based tool, the AutoDep Input Tool (ADIT;
http://pdb.rutgers.edu/adit/), was introduced for the easy deposition of
data. The BNL-developed tool, AutoDep, was ported to the RCSB site to
allow
people to complete depositions started at the BNL site and to provide
continuity.  For all data deposited, the RCSB has developed a much faster
data processing system that reduces the processing time by a factor of ten
to assure the timely access of information by the community of users. The
RCSB also began accepting data collected and processed at remote sites,
the
first one being at the European Bioinformatics Institute in Hinxton,
England. 

The RCSB has released two new search engines: SearchLite and SearchFields.
SearchLite allows simple text-based searches while SearchFields allows
searches to be done on specific data items stored in the database. Both
have
very rich reporting capabilities that include a Structure Explorer page
with
summary information about each structure, reports about the geometric
features of the structures, and structure neighboring. Cross-links to
other
databases are also provided.

The RCSB supports two ftp archives: ftp://ftp.rcsb.org, a reorganized and
more logical organization of all PDB data, software, and documentation;
and
ftp://bnlarchive.rcsb.org, a near-identical copy  of the original BNL
archive for BNL-style PDB mirrors. The new RCSB-style mirrors being
established around the world will contain the flat file data as well as
the
full database of information.
The RCSB is a consortium composed of Rutgers, the State University of New
Jersey; the University of California at San Diego (UCSD); and the National
Institute of Standards and Technology (NIST). The project runs under a
Cooperative Agreement from the National Science Foundation (NSF), with
funding from that agency as well as the Department of Energy, and two
units
of the National Institutes of Health: the National Institute of General
Medical Sciences and the National Library of Medicine.  The
responsibilities
of the three sites have been divided according to experience and
expertise.


Principal investigator Helen Berman, a member of the Biophysical Society
and Rutgers professor of chemistry, was part of the original team that
developed the PDB at Brookhaven in 1971. She is responsible for the
development of the  Nucleic Acid Database (NDB) at Rutgers, which
assembles
and distributes structural information about nucleic acids and contains an
atlas, an archive and a sophisticated search engine to access the data. In
collaboration with John Westbrook, who has played a key role in the
development of the mmCIF dictionary, they have drawn on the experiences
with
the NDB and have led a team of people who have created a new data
deposition
and processing system for all macromolecules.

At the San Diego Supercomputer Center (SDSC) at UCSD, senior principal
scientist and adjunct professor Phil Bourne leads a group of scientists in
the Biological Data Representation and Query Initiative. The group has
developed locally a number of databases containing derived data on protein
structures and maintains a mirror site of Berman's NDB. Recent work
produced a database of structure comparisons for the more than 10,000
structures in the PDB. Together with Peter Arzberger, a computational
biologist and Executive Director of NPACI, this group will be responsible
for all aspects of data query and distribution.

Gary L. Gilliland, chief of the Biotechnology Division in NIST's Chemical
Science and Technology Laboratory, will lead the NIST effort. He has
maintained an active research program in protein crystallography for more
than 20 years. Gilliland also played a key role in establishing the Center
for Advanced Research in Biotechnology (CARB), a joint effort of NIST and
the University of Maryland Biotechnology Institute, where he served as the
Associate Director until 1996. Phoebe Fagan, who has worked for many years
in the NIST Standard Reference Data program, is responsible for the
technical aspects of the project at that site. NIST will establish data
uniformity of the old and new structures in order to improve the
accessibility and reliability of queries and will also manage the Master
Archive. 

The creation of this resource was both exciting and demanding.  The
successful culmination of the transition of the PDB from BNL to the RCSB
required the dedication and cooperation of the members of the RCSB team,
the
staff at Brookhaven National Laboratory led by Joel Sussman, and the
federal
agencies who fund the PDB. 

.