Real World Experiences in Operating a Collaboratory: The Protein Data Bank

1
Real World Experiences in Operating a
Collaboratory The Protein Data Bank

• Helen M. Berman
• Board of Governors Professor of Chemistry
  Chemical BiologyDirector, Research Collaboratory
  for Structural Bioinformatics and the Protein
  Data Bank

2
What is the PDB?

• Single international repository for all
  information about the structure of large
  biological molecules
• Archival database with hundreds of thousands of
  users who depend on the data

3
(No Transcript)
4
Number of released entries
Year
5
1970s

• Grass roots community efforts to archive data
• Protein crystallographers discuss how to archive
  data
• June 1971
• Cold Spring Harbor meeting brings groups together
• (Cold Spring Harbor Symposia on Quantitative
  Biology, vol. XXXVI, 1972.)
• October 1971
• PDB is announced in Nature New Biology
• (7 structures vol 233, 1971, page 223)
• 1975
• PDB receives first funding from NSF (32
  structures)

6
(No Transcript)
7
Nature New Biology
8
1980s

• Technology takes off
• molecular biology, instrumentation, computer
  hardware and software
• Structural biology is able to focus on medical
  problems
• Community efforts to promote data sharing
• IUCr guidelines requiring data deposition in the
  PDB are published

9
1990s

• Number of structures increases exponentially
• Complexity of structures increases
• New databases begin to emerge
• More structures determined by cryo- electron
  microscopy
• Plans for structural genomics emerge
• User community for the PDB expands dramatically

RCSB awarded contract for the PDB
10
(No Transcript)
11
Who does what?

• Rutgers
• Data in standards, validation, annotation
• UCSD/SDSC
• Data out search engine, Web site, data
  distribution

12
(No Transcript)
13
(No Transcript)
14
Communication

• VTC
• Electronic email, forums, wikis
• Procedures
• Internal newsletter
• Retreats

15
Retreats

• Team building exercises
• Management training
• Technical discussions
• Time to get to know one another

16
(No Transcript)
17
VTCs

• Two formal ones per week
• Ad hoc when there are issues to discuss

18
2000s

• Continued growth in structure studies
• Structural genomics takes off
• RCSB PDB contract renewed

BMRB joins RCSB

• Release of new database and website

2bus
Kurt Wüthrich, who determined the first first
three-dimensional protein structure by NMR
spectroscopy with coworkers (proteinase IIa
inhibitor from bull seminal plasma) was awarded
the Nobel Prize in Chemistry in 2002
19
(No Transcript)
20
The PDB is Global
21
Worldwide Protein Data Bank www.wwpdb.org
22
Mission

• Maintain a single archive of macromolecular
  structural data that is freely and openly
  available to the global community

23
(No Transcript)
24
(No Transcript)
25
wwPDB

• Formalization of current working practice
• Members
• RCSB PDB (Research Collaboratory for Structural
  Bioinformatics)
• PDBj (Osaka University)
• Macromolecular Structure Database (EBI)
• MOU signed July 1, 2003
• Announced in Nature Structural Biology
  November 21, 2003

26
Guidelines and Responsibilities

• All members issue PDB IDs and serve as
  distribution sites for data
• One member is the archive keeper (RCSB)
• All format documentation publicly available
• Strict rules for redistribution of PDB files
• All sites can create their own web sites

27
Future

• 60,000 structures by 2008
• 20,000 depositions per year in 2010
• Complexity will increase dramatically
• New methods will yield new structures

28
Scientific Challenges

• Number of data files continues to increase
• Information content of each data file is
  increasing
• Many more very large macromolecular complexes
• New structure determination methods
• Structure genomics

29
Technical Challenges

• How do we represent diverse data?
• How do make a searchable database?
• How do we integrate with other data resources?
• How do we make a scalable system?
• How do we meet the needs of a diverse community?

30
Structural Genomics
The next step beyond the human genome project
From the NIH Request for Proposals for Structure
Genomics Centers
These studies should lead to an understanding of
structure/function relationships and the ability
to obtain structural models of all proteins
identified by genomics. This project will require
the determination of a large number of protein
structures in a high-throughput mode.
31
PSI - Structures (Sep-2005 1246 images)
32
Community

• Depositors
• Different methods X-ray, NMR, cryo-EM
• Users
• Specialists (structural biologists)
• Generalists
• Educators
• Students
• Lay community

33
Active Outreach

• Electronic
• Meetings
• Publications
• One on one
• Many workshops

34
Issues

• Standards What is the role of the centers? What
  should it be?
• Long term preservation How long? What are the
  options?
• Stability Strong dependency of research
  community demands a more stable model

35
Bottom line

• All the interdependencies within wwPDB and
  between the scientific community and wwPDB call
  for a new funding model that will ensure the long
  term preservation and availability of the
  research data contained within these resources

36
Acknowledgements
Operated by two members of the RCSB
The RCSB PDB is a member of the
Supported by