Transcript No Slide Title

Update on PDB Data Deposition
Specifications
http://www.pdb.org/ • [email protected]
Defining SG Deposition Content
• Preliminary recommendations from the International
Task Force on Deposition, Archiving, and Curation of
Primary Information for Structural Genomics (Helen M.
Berman & Geoff Barton, Chairs, and many participants)
• Extensions from the Working Group on Structural
Genomics Data Deposition
• Significant participation from all Structural
Genomics Projects
• Workshops
Task Force Members
Helen M. Berman (Chair)
Ge off Barton (Co-Chair)
Rutgers University (US)
EMBL-European Bioinformatics
In stitute (UK)
Stephen Burley
Andrzej Joachimiak
Haruki Nakamura
Eldon Ulrich
The Rockefeller University (US)
Argonne National Lab (US)
Osaka University (Japan)
BioMagResBank (US)
Aled Edwards
Sung-Hou Kim
John Rose
Bi-Cheng Wang
Banting and Best Department
of Medical Research (Canada)
University of Calif ornia,
Berkeley (US)
University of Georgia (US)
University of Georgia (US)
Udo Heinemann
Ga etano Montelione
Joel Sussman
Ian Wilson
Max-Delbruck Center f or
Molecular Medicine (Germany)
Rutgers University (US)
Weizmann Institute of Science
(Israel)
The Scripps Research Institute
(US)
Osnat Herzberg
Dino Moras
Thomas C Terwilliger
Shigeyuki Yokoyama
Center for Advanced Research
in Biotechnology (US)
IGBMC (France)
Los Alamos National Lab (US)
Genomic Sciences Centre
(Japan)
Data Dictionary Working Group
and Major Contributors
Paul Adams
Jonathan Diprose
Kim Henrick
Lawrence Berkeley Labs (US)
Oxford Protein Production
Facility (UK)
MSD- European
Bioinformatics Institute (UK)
Eldon Ulrich
Charles Weeks
BioMagResBank
University Wisconsin (US)
Hauptman-Woodward Institute (US)
Rosalind Kim
Cathy Lawson
Berkeley Structural Genomics Center (US)
Rutgers University (US)
John Ionides
John Westbrook
MSD-European Bioinformatics Institute (UK)
PDB - Rutgers University (US)
Workshops
Interdisciplinary Workshop promoting collaboration in
high-throughput X-ray structure determination
March 22-23, 2002, Santa Fe, New Mexico, USA
Organizers: Tom Terwilliger, Paul Adams, Samar Hasnain
Sponsor: Institute for Complex Adaptive Matter
and the International Structural Genomics Organization
Structural Genomics Informatics and Software Integration
Workshop
May 24-25, 2002, Hyatt Regency San Antonio
Organizers: Helen M. Berman, Tom Terwilliger, John Westbrook
Sponsors: National Institute of General Medical Sciences and
International Structural Genomics Organization
Current Data Dictionaries
http://deposit.pdb.org/mmcif/
• PDB data exchange
– Including structural genomics and data harvesting
extensions
• mmCIF
• NMR
• Modeling
• Crystallization
• Symmetry
• Image data
• BIOSYNC
Dictionary Extensions for
Structural Genomics
Guiding Principles
• Data deposited will be at the level of journal
“materials and methods” section
• Each data item must be carefully defined in
PDB exchange data dictionary
X-ray Deposition Specifications
• Content includes: macromolecular naming, source
organism, crystallization and cell parameters, data
collection, structure solution and phasing, model building,
refinement
• Significant additions beyond current PDB deposition
content in data collection, phasing and model building
• Additional description of multi-method phasing
experiments
• X-ray data items map closely to the output provided from
existing structure determination applications and are easily
extracted
NMR Specifications
• Content includes: macromolecular naming; source
organism; sample description; experimental conditions
and data collection; structure solution; constraints, force
constants and related statistics; ensemble details and
statistics
• Significant additions beyond current PDB deposition
content in the details sample preparation, constraints, and
all related statistics
• NMR data items map closely to the output provided from
existing structure determination applications
Protein Production Specifications
• Content includes: target identification, source
information, gene production, bacterial cloning,
bacterial expression, purification
• Specifications attempt to integrate with existing
LIMS
• Virtually all new content for deposition
Measurable Success
Direct mmCIF depositions conforming to exchange
dictionary fully annotated in 15 minutes
Next Steps
• X-ray
–
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–
–
Dictionary ready for approval
PDB deposition specifications are well supported in applications
Extraction tools available to collect data items not exported in CIF
New multi-method phasing data items require testing
• NMR
– Dictionary ready for approval
– PDB deposition specifications are well supported in applications
– Better direct support for NMRstar/NMRif and data extraction tools
are needed
• Protein Production
– Data dictionary drafted
– Deposition specifications require testing and will need to be
integrated with project LIMS
Access
PDB Data Dictionaries and mmCIF Resource Site
http://deposit.pdb.org/mmcif/
PDB TargetDB site
http://targetdb.pdb.org/
PDB Structural Genomics Resource Page
http://www.rcsb.org/pdb/strucgen.html
PDB Software Download Site
http://deposit.pdb.org/software/
mmCIF Beta Data Site
ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmcif/
PDB Deposition Sites
http://autodep.ebi.ac.uk/
http://pdbdep.protein.osaka-u.ac.jp/adit/
http://deposit.pdb.org/adit/