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Volume 28
Issue 1
1 January 2000
Article Contents
• Abstract
• INTRODUCTION
• DATA ACQUISITION AND PROCESSING
• THE PDB DATABASE RESOURCE
• DATA DISTRIBUTION
• DATA ARCHIVING
• MAINTENANCE OF THE LEGACY BNL SYSTEM
• CURRENT DEVELOPMENTS
• PDB ADVISORY BOARDS
• FOR FURTHER INFORMATION
• CONCLUSION
• ACKNOWLEDGEMENTS
• References
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Nucleic Acids Research

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Science and Mathematics

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JOURNAL ARTICLE

The Protein Data Bank

Helen M. Berman, John Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N.
Shindyalov, Philip E. Bourne

Nucleic Acids Research, Volume 28, Issue 1, 1 January 2000, Pages 235–242,
https://doi.org/10.1093/nar/28.1.235
Published:

01 January 2000

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Abstract
The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide
archive of structural data of biological macromolecules. This paper describes the goals
of the PDB, the systems in place for data deposition and access, how to obtain further
information, and near-term plans for the future development of the resource.
Issue Section:
Article
Received September 20, 1999; Revised and Accepted October 17, 1999.

INTRODUCTION
The Protein Data Bank (PDB) was established at Brookhaven National Laboratories
(BNL) (1) in 1971 as an archive for biological macromolecular crystal structures. In the
beginning the archive held seven structures, and with each year a handful more were
deposited. In the 1980s the number of deposited structures began to increase
dramatically. This was due to the improved technology for all aspects of the
crystallographic process, the addition of structures determined by nuclear magnetic
resonance (NMR) methods, and changes in the community views about data sharing.
By the early 1990s the majority of journals required a PDB accession code and at least
one funding agency (National Institute of General Medical Sciences) adopted the
guidelines published by the International Union of Crystallography (IUCr) requiring
data deposition for all structures.

The mode of access to PDB data has changed over the years as a result of improved
technology, notably the availability of the WWW replacing distribution solely via
magnetic media. Further, the need to analyze diverse data sets required the
development of modern data management systems.

Initial use of the PDB had been limited to a small group of experts involved in
structural research. Today depositors to the PDB have varying expertise in the
techniques of X-ray crystal structure determination, NMR, cryoelectron microscopy
and theoretical modeling. Users are a very diverse group of researchers in biology,
chemistry and computer scientists, educators, and students at all levels. The
tremendous influx of data soon to be fueled by the structural genomics initiative, and
the increased recognition of the value of the data toward understanding biological
function, demand new ways to collect, organize and distribute the data.

In October 1998, the management of the PDB became the responsibility of the
Research Collaboratory for Structural Bioinformatics (RCSB). In general terms, the
vision of the RCSB is to create a resource based on the most modern technology that
facilitates the use and analysis of structural data and thus creates an enabling
resource for biological research. Specifically in this paper, we describe the current
procedures for data deposition, data processing and data distribution of PDB data by
the RCSB. In addition, we address the issues of data uniformity. We conclude with
some current developments of the PDB.

DATA ACQUISITION AND PROCESSING

A key component of creating the public archive of information is the efficient capture
and curation of the data—data processing. Data processing consists of data
deposition, annotation and validation. These steps are part of the fully documented
and integrated data processing system shown in Figure 1.

In the present system (Fig. 2), data (atomic coordinates, structure factors and NMR
restraints) may be submitted via email or via the AutoDep Input Tool (ADIT;
http://pdb.rutgers. edu/adit/ ) developed by the RCSB. ADIT, which is also used to
process the entries, is built on top of the mmCIF dictionary which is an ontology of
1700 terms that define the macro-molecular structure and the crystallographic
experiment (2,3), and a data processing program called MAXIT (MAcromolecular
EXchange Input Tool). This integrated system helps to ensure that the data submitted
are consistent with the mmCIF dictionary which defines data types, enumerates
ranges of allowable values where possible and describes allowable relationships
between data values.
After a structure has been deposited using ADIT, a PDB identifier is sent to the author
automatically and immediately (Fig. 1, Step 1). This is the first stage in which
information about the structure is loaded into the internal core database (see section
on the PDB Database Resource). The entry is then annotated as described in the
validation section below. This process involves using ADIT to help diagnose errors or
inconsistencies in the files. The completely annotated entry as it will appear in the
PDB resource, together with the validation information, is sent back to the depositor
(Step 2). After reviewing the processed file, the author sends any revisions (Step 3).
Depending on the nature of these revisions, Steps 2 and 3 may be repeated. Once
approval is received from the author (Step 4), the entry and the tables in the internal
core database are ready for distribution. The schema of this core database is a subset
of the conceptual schema specified by the mmCIF dictionary.

All aspects of data processing, including communications with the author, are
recorded and stored in the correspondence archive. This makes it possible for the PDB
staff to retrieve information about any aspect of the deposition process and to closely
monitor the efficiency of PDB operations.

Current status information, comprised of a list of authors, title and release category,
is stored for each entry in the core database and is made accessible for query via the
WWW interface (http://www.rcsb.org/pdb/status.html ). Entries before release are
categorized as ‘in processing’ (PROC), ‘in depositor review’ (WAIT), ‘to be held until
publication’ (HPUB) or ‘on hold until a depositor-specified date’ (HOLD).

Content of the data collected by the PDB

All the data collected from depositors by the PDB are considered primary data.
Primary data contain, in addition to the coordinates, general information required for
all deposited structures and information specific to the method of structure
determination. Table 1 contains the general information that the PDB collects for all
structures as well as the additional information collected for those structures
determined by X-ray methods. The additional items listed for the NMR structures are
derived from the International Union of Pure and Applied Chemistry
recommen-dations (IUPAC) (4) and will be implemented in the near future.

The information content of data submitted by the depositor is likely to change as new
methods for data collection, structure determination and refinement evolve and
advance. In addition, the ways in which these data are captured are likely to change as
the software for structure determination and refinement produce the necessary data
items as part of their output. ADIT, the data input system for the PDB, has been
designed so as to easily incorporate these likely changes.

Validation
Validation refers to the procedure for assessing the quality of deposited atomic
models (structure validation) and for assessing how well these models fit the
experimental data (experimental validation). The PDB validates structures using
accepted community standards as part of ADIT’s integrated data processing system.
The following checks are run and are summarized in a letter that is communicated
directly to the depositor:

Covalent bond distances and angles. Proteins are compared against standard values
from Engh and Huber (5); nucleic acid bases are compared against standard values
from Clowney et al. (6); sugar and phosphates are compared against standard values
from Gelbin et al. (7).

Stereochemical validation. All chiral centers of proteins and nucleic acids are checked
for correct stereochemistry.

Atom nomenclature. The nomenclature of all atoms is checked for compliance with
IUPAC standards (8) and is adjusted if necessary.

Close contacts. The distances between all atoms within the asymmetric unit of crystal
structures and the unique molecule of NMR structures are calculated. For crystal
structures, contacts between symmetry-related molecules are checked as well.

Ligand and atom nomenclature. Residue and atom nomen-clature is compared against
the PDB dictionary (ftp://ftp.rcsb. org/pub/pdb/data/monomers/het_dictionary.txt )
for all ligands as well as standard residues and bases. Unrecognized ligand groups are
flagged and any discrepancies in known ligands are listed as extra or missing atoms.

Sequence comparison. The sequence given in the PDB SEQRES records is compared
against the sequence derived from the coordinate records. This information is
displayed in a table where any differences or missing residues are marked. During
structure processing, the sequence database references given by DBREF and SEQADV
are checked for accuracy. If no reference is given, a BLAST (9) search is used to find
the best match. Any conflict between the PDB SEQRES records and the sequence
derived from the coordinate records is resolved by comparison with various sequence
databases.

Distant waters. The distances between all water oxygen atoms and all polar atoms
(oxygen and nitrogen) of the macromolecules, ligands and solvent in the asymmetric
unit are calculated. Distant solvent atoms are repositioned using crystallographic
symmetry such that they fall within the solvation sphere of the macromolecule.

In almost all cases, serious errors detected by these checks are corrected through
annotation and correspondence with the authors.

It is also possible to run these validation checks against structures before they are
deposited. A validation server (http://pdb.rutgers.edu/validate/ ) has been made
available for this purpose. In addition to the summary report letter, the server also
provides output from PROCHECK (10), NUCheck (Rutgers University, 1998) and
SFCHECK (11). A summary atlas page and molecular graphics are also produced.
The PDB will continually review the checking methods used and will integrate new
procedures as they are developed by the PDB and members of the scientific
community.

Other data deposition centers

The PDB is working with other groups to set up deposition centers. This enables
people at other sites to more easily deposit their data via the Internet. Because it is
critical that the final archive is kept uniform, the content and format of the final files
as well as the methods used to check them must be the same. At present, the European
Bioinformatics Institute (EBI) processes data that are submitted to them via AutoDep
(http://autodep.ebi.ac.uk/ ). Once these data are processed they are sent to the RCSB in
PDB format for inclusion in the central archive. Before this system was put in place it
was tested to ensure consistency among entries in the PDB archive. In the future, the
data will be exchanged in mmCIF format using a common exchange dictionary, which
along with standardized annotation procedures will ensure a high degree of
uniformity in the archival data. Structures deposited and processed at the EBI
represent ~20% of all data deposited.

Data deposition will also soon be available from an ADIT Web site at The Institute for
Protein Research at Osaka University in Japan. At first, structures deposited at this site
will be processed by the PDB staff. In time, the staff at Osaka will complete the data
processing for these entries and send the files to the PDB for release.

NMR data
The PDB staff recognizes that NMR data needs a special development effort.
Historically these data have been retrofitted into a PDB format defined around
crystallographic information. As a first step towards improving this situation, the PDB
did an extensive assessment of the current NMR holdings and presented their findings
to a Task Force consisting of a cross section of NMR researchers. The PDB is working
with this group, the BioMagResBank (BMRB) (12), as well as other members of the
NMR community, to develop an NMR data dictionary along with deposition and
validation tools specific for NMR structures. This dictionary contains among other
items descriptions of the solution components, the experimental conditions,
enumerated lists of the instruments used, as well as information about structure
refinement.

Data processing statistics

Production processing of PDB entries by the RCSB began on January 27, 1999. The
median time from deposition to the completion of data processing including author
interactions is less than 10 days. The number of structures with a HOLD release status
remains at ~22% of all submissions; 28% are held until publication; and 50% are
released immediately after processing.
When the RCSB became fully responsible there were about 900 structures that had not
been completely processed. These included so called Layer 1 structures that had been
processed by computer software but had not been fully annotated. All of these
structures have now been processed and are being released after author review.

The breakdown of the types of structures in the PDB is shown in Table 2. As of

September 14, 1999, the PDB contained 10 714 publicly accessible structures with
another 1169 entries on hold. Of these, 8789 (82%) were determined by X-ray
methods, 1692 (16%) were determined by NMR and 233 (2%) were theoretical models.
Overall, 35% of the entries have deposited experimental data.

Data uniformity
A key goal of the PDB is to make the archive as consistent and error-free as possible.
All current depositions are reviewed carefully by the staff before release. Tables of
features are generated from the internal data processing database and checked. Errors
found subsequent to release by authors and PDB users are addressed as rapidly as
possible. Corrections and updates to entries should be sent to deposit@rcsb.
rutgers.edu for the changes to be implemented and re-released into the PDB archive.

One of the most difficult problems that the PDB now faces is that the legacy files are
not uniform. Historically, existing data (‘legacy data’) comply with several different
PDB formats and variation exists in how the same features are described for different
structures within each format. The introduction of the advanced querying capabilities
of the PDB makes it critical to accelerate the data uniformity process for these data.
We are now at a stage where the query capabilities surpass the quality of the
underlying data. The data uniformity project is being approached in two ways.
Families of individual structures are being reprocessed using ADIT. The strategy of
processing data files as groups of similar structures facilitates the application of
biological knowledge by the annotators. In addition, we are examining particular
records across all entries in the archive. As an example, we have recently completed
examining and correcting the chemical descriptions of all of the ligands in the PDB.
These corrections are being entered in the database. The practical consequence of this
is that soon it will be possible to accurately find all the structures in the PDB bound to
a particular ligand or ligand type. In addition to the efforts of the PDB to remediate the
older entries, the EBI has also corrected many of the records in the PDB as part of their
‘clean-up’ project. The task of integrating all of these corrections done at both sites is
very large and it is essential that there is a well-defined exchange format to do this;
mmCIF will be used for this purpose.

THE PDB DATABASE RESOURCE

The database architecture
In recognition of the fact that no single architecture can fully express and efficiently
make available the information content of the PDB, an integrated system of
heterogeneous databases has been created that store and organize the structural data.
At present there are five major components (Fig. 3):

• The core relational database managed by Sybase (Sybase SQL server release 11.0,
Emeryville, CA) provides the central physical storage for the primary experimental
and coordinate data described in Table 1. The core PDB relational database contains all
deposited information in a tabular form that can be accessed across any number of
structures.

• The final curated data files (in PDB and mmCIF formats) and data dictionaries are
the archival data and are present as ASCII files in the ftp archive.

• The POM (Property Object Model)-based databases, which consist of indexed objects
containing native (e.g., atomic coordinates) and derived properties (e.g., calculated
secondary structure assignments and property profiles). Some properties require no
derivation, for example, B factors; others must be derived, for example, exposure of
each amino acid residue (13) or Cα contact maps. Properties requiring significant
computation time, such as structure neighbors (14), are pre-calculated when the
database is incremented to save considerable user access time.

• The Biological Macromolecule Crystallization Database (BMCD; 15) is organized as a

relational database within Sybase and contains three general categories of literature
derived information: macromolecular, crystal and summary data.

• The Netscape LDAP server is used to index the textual content of the PDB in a
structured format and provides support for keyword searches.

It is critical that the intricacies of the underlying physical databases be transparent to

the user. In the current implementation, communication among databases has been
accomplished using the Common Gateway Interface (CGI). An integrated Web
interface dispatches a query to the appropriate database(s), which then execute the
query. Each database returns the PDB identifiers that satisfy the query, and the CGI
program integrates the results. Complex queries are performed by repeating the
process and having the interface program perform the appropriate Boolean
operation(s) on the collection of query results. A variety of output options are then
available for use with the final list of selected structures.

The CGI approach [and in the future a CORBA (Common Object Request Broker
Architecture)-based approach] will permit other databases to be integrated into this
system, for example extended data on different protein families. The same approach
could also be applied to include NMR data found in the BMRB or data found in other
community databases.

Database query
Three distinct query interfaces are available for the query of data within PDB: Status
Query (http://www.rcsb.org/pdb/status.html ), SearchLite
(http://www.rcsb.org/pdb/searchlite.html ) and Search-Fields
(http://www.rscb.org/pdb/queryForm.cgi ). Table 3summarizes the current query and
analysis capabilities of the PDB. Figure 4 illustrates how the various query options are
organized.

SearchLite, which provides a single form field for keyword searches, was introduced
in February 1999. All textual information within the PDB files as well as dates and
some experimental data are accessible via simple or structured queries. SearchFields,
accessible since May 1999, is a customizable query form that allows searching over
many different data items including compound, citation authors, sequence (via a
FASTA search; 16) and release or deposition dates.

Two user interfaces provide extensive information for result sets from SearchLite or
SearchFields queries. The ‘Query Result Browser’ interface allows for access to some
general information, more detailed information in tabular format, and the possibility
to download whole sets of data files for result sets consisting of multiple PDB entries.
The ‘Structure Explorer’ interface provides information about individual structures as
well as cross-links to many external resources for macromolecular structure data
(Table 4). Both interfaces are accessible to other data resources through the simple
CGI application programmer interface (API) described at http://www.
rcsb.org/pdb/linking.html

The websiteusage has climbed dramatically since the system was first introduced in
February 1999 (Table 5). As of November 1, 1999, the main PDB site receives, on
average, greater than one hit per second and greater than one query per minute.

DATA DISTRIBUTION
The PDB distributes coordinate data, structure factor files and NMR constraint files. In
addition it provides documentation and derived data. The coordinate data are
distributed in PDB and mmCIF formats. Currently, the PDB file is created as the final
product of data annotation; the program pdb2cif (17) is used to generate the mmCIF
data. This program is used to accommodate the legacy data. In the future, both the
mmCIF and PDB format files created during data annotation will be distributed.

Data are distributed to the community in the following ways:

• From primary PDB Web and ftp sites at UCSD, Rutgers and NIST that are updated
weekly.

• From complete Web-based mirror sites that contain all databases, data files,
documentation and query interfaces updated weekly.

• From ftp-only mirror sites that contain a complete or subset copy of data files,
updated at intervals defined by the mirror site. The steps necessary to create an ftp-
only mirror site are described in http://www.rcsb.org/pdb/ftpproc.final.html
• Quarterly CD-ROM.

Data are distributed once per week. New data officially become available at 1 a.m. PST
each Wednesday. This follows the tradition developed by BNL and has minimized the
impact of the transition on existing mirror sites. Since May 1999, two ftp archives
have been provided: 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 which is maintained for purposes of
backward compatibility. RCSB-style PDB mirrors have been established in Japan
(Osaka University), Singapore (National University Hospital) and in UK (the
Cambridge Crystallographic Data Centre). Plans call for operating mirrors in Brazil,
Australia, Canada, Germany, and possibly India.

The first PDB CD-ROM distribution by the RCSB contained the coordinate files,
experimental data, software and documentation as found in the PDB on June 30, 1999.
Data are currently distributed as compressed files using the compression utility
program gzip. Refer to http://www.rcsb.org/pdb/cdrom.html for details of how to
order CD-ROM sets. There is presently no charge for this service.

DATA ARCHIVING
The PDB is establishing a central Master Archiving facility. The Master Archive plan is
based on five goals: reconstruction of the current archive in case of a major disaster;
duplication of the contents of the PDB as it existed on a specific date; preservation of
software, derived data, ancillary data and all other computerized and printed
information; automatic archiving of all depositions and the PDB production resource;
and maintenance of the PDB correspondence archive that documents all aspects of
deposition. During the transition period, all physical materials including electronic
media and hard copy materials were inventoried and stored, and are being catalogued.

MAINTENANCE OF THE LEGACY BNL SYSTEM

One of the goals of the PDB has been to provide a smooth transition from the system
at BNL to the new system. Accordingly, AutoDep, which was developed by BNL (18) for
data deposition, has been ported to the RCSB site and enables depositors to complete
in-progress depositions as well as to make new depositions. In addition, the EBI
accepts data using AutoDep. Similarly, the programs developed at BNL for data query
and distribution (PDBLite, 3DBbrowser, etc.) are being maintained by the remaining
BNL-style mirrors. The RCSB provides data in a form usable by these mirrors. Finally
the style and format of the BNL ftp archive is being maintained at ftp://bnlarchive.
rcsb.org

A multitude of resources and programs depend upon their links to the PDB. To
eliminate the risk of interruption to these services, links to the PDB at BNL were
automatically redirected to the RCSB after BNL closed operations on June 30, 1999
using a network redirect implemented jointly by RCSB and BNL staff. While this
redirect will be maintained, external resources linking to the PDB are advised to
change any URLs from http://www.pdb.bnl.gov/ to http://www.rcsb.org/

CURRENT DEVELOPMENTS
In the coming months, the PDB plans to continue to improve and develop all aspects
of data processing. Deposition will be made easier, and annotation will be more
automated. In addition, software for data deposition and validation will be made
available for in-laboratory use.

The PDB will also continue to develop ways of exchanging information between
databases. The PDB is leading the Object Management Group Life Sciences Initiative’s
efforts to define a CORBA interface definition for the representation of
macromolecular structure data. This is a standard developed under a strict procedure
to ensure maximum input by members of various academic and industrial research
communities. At this stage, proposals for the interface definition, including a working
prototype that uses the standard, are being accepted. For further details refer to
http://www.omg.org/cgi-bin/doc?lifesci/ 99-08-15 . The finalized standard interface
will facilitate the query and exchange of structural information not just at the level of
complete structures, but at finer levels of detail. The standard being proposed by the
PDB will conform closely to the mmCIF standard. It is recognized that other forms of
data representation are desirable, for example using eXtensible Markup Language
(XML). The PDB will continue to work with mmCIF as the underlying standard from
which CORBA and XML representations can be generated as dictated by the needs of
the community.

The PDB will also develop the means and methods of communications with the broad
PDB user community via the Web. To date we have developed prototype protein
documentaries (19) that explore this new medium in describing structure–function
relationships in proteins. It is also possible to develop educational materials that will
run using a recent Web browser (20).

Finally it is recognized that structures exist both in the public and private domains. To
this end we are planning on providing a subset of database tools for local use. Users
will be able to load both public and proprietary data and use the same search and
exploratory tools used at PDB resources.

The PDB does not exist in isolation, rather each structure represents a point in a
spectrum of information that runs from the recognition of an open reading frame to a
fully understood role of the single or multiple biological functions of that molecule.
The available information that exists on this spectrum changes over time.
Recognizing this, the PDB has developed a scheme for the dynamic update of a variety
of links on each structure to whatever else can be automatically located on the
Internet. This information is itself stored in a database and can be queried. This
feature will appear in the coming months to supplement the existing list of static links
to a small number of the more well known related Internet resources.
PDB ADVISORY BOARDS
The PDB has several advisory boards. Each member institution of the RCSB has its
own local PDB Advisory Committee. Each institution is responsible for implementing
the recommendations of those committees, as well as the recommendations of an
International Advisory Board. Initially, the RCSB presented a report to the Advisory
Board previously convened by BNL. At their recommendation, a new Board has been
approached which contains previous members and new members. The goal was to
have the Board accurately reflect the depositor and user communities and thus include
experts from many disciplines.

Serious issues of policy are referred to the major scientific societies, notably the IUCr.
The goal is to make decisions based on input from a broad international community of
experts. The IUCr maintains the mmCIF dictionary as the data standard upon which
the PDB is built.

FOR FURTHER INFORMATION

The PDB seeks to keep the community informed of new develop-ments via weekly
news updates to the Web site, quarterly newsletters, and a soon to be initiated annual
report. Users can request information at any time by sending mail to info@rcsb. org .
Finally, the pdb-l@rcsb.org listserver provides a community forum for the discussion
of PDB-related issues. Changes to PDB operations that may affect the community, for
example, data format changes, are posted here and users have 60 days to discuss the
issue before changes are made according to major consensus. Table 6indicates how to
access these resources.

CONCLUSION
These are exciting and challenging times to be responsible for the collection, curation
and distribution of macromolecular structure data. Since the RCSB assumed
responsibility for data deposition in February 1999, the number of depositions has
averaged approximately 50 per week. However, with the advent of a number of
structure genomics initiatives worldwide this number is likely to increase. We
estimate that the PDB, which at this writing contains approximately 10 500
structures, could triple or quadruple in size over the next 5 years. This presents a
challenge to timely distribution while maintaining high quality. The PDB’s approach
of using modern data management practices should permit us to scale to
accommodate a large data influx.

The maintenance and further development of the PDB are community efforts. The
willingness of others to share ideas, software and data provides a depth to the
resource not obtainable otherwise. Some of these efforts are acknowledged below.
New input is constantly being sought and the PDB invites you to make comments at
any time by sending electronic mail to info@rcsb.org
ACKNOWLEDGEMENTS
Research Collaboratory for Structural Bioinformatics (RCSB) is a consortium
consisting of three institutions: Rutgers University, San Diego Supercomputer Center
at University of California, San Diego, and the National Institute of Standards and
Technology. The current RCSB PDB staff include the authors indicated and Kyle
Burkhardt, Anke Gelbin, Michael Huang, Shri Jain, Rachel Kramer, Nate Macapagal,
Victoria Colflesh, Bohdan Schneider, Kata Schneider, Christine Zardecki (Rutgers);
Phoebe Fagan, Diane Hancock, Narmada Thanki, Michael Tung, Greg Vasquez (NIST);
Peter Arzberger, John Badger, Douglas S. Greer, Michael Gribskov, John Kowalski,
Glen Otero, Shawn Strande, Lynn F. Ten Eyck, Kenneth Yoshimoto (UCSD). The
continuing support of Ken Breslauer (Rutgers), John Rumble (NIST) and Sid Karin
(SDSC) is gratefully acknowledged. Current collaborators contributing to the future
development of the PDB are the BioMagResBank, the Cambridge Crystallographic
Data Centre, the HIV Protease Database Group, The Institute for Protein Research,
Osaka University, National Center for Biotechnology Information, the ReLiBase
developers, and the Swiss Institute for Bio-informatics/Glaxo. We are especially
grateful to Kim Henrick of the EBI and Steve Bryant at NCBI who have reviewed our
files and sent back constructive criticisms. This has helped the PDB to continuously
improve its procedures for producing entries. The cooperation of the BNL PDB staff is
gratefully acknowledged. Portions of this article will appear in Volume F of the
International Tables of Crystallography. This work is supported by grants from the
National Science Foundation, the Office of Biology and Environmental Research at the
Department of Energy, and two units of the National Institutes of Health: the National
Institute of General Medical Sciences and the National Institute of Medicine.

*
To whom correspondence should be addressed at: Department of Chemistry, Rutgers University, 610
Taylor Road, Piscataway, NJ 08854-8087, USA. Tel: +1 732 445 4667; Fax: +1 732 445 4320; Email:
berman@rcsb.rutgers.edu

Open in new tabDownload slide

Figure 1. The steps in PDB data processing. Ellipses represent actions and rectangles define content.

Open in new tabDownload slide

Figure 2. The integrated tools of the PDB data processing system.

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Figure 3. The integrated query interface to the PDB.

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Figure 4. The various query options that are available for the PDB.

Table 1.

Content of data in the PDB

TABLE CRC: gkd090tol
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Table 2.

Demographics of data in the PDB

TABLE CRC: gkd090to2
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Table 3.

Current query capabilities of the PDB

TABLE CRC: gkd090to3
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Table 4.

Static cross-links to other data resources currently provided by the PDB

TABLE CRC: gkd090t04
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Table 5.

Web query statistics for the primary RCSB site (http://www.rcsb.org )

TABLE CRC: gkd090to5
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Table 6.
PDB information sources
TABLE CRC: gkd090to6
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References
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