Www.pdb.org [email protected] Real World Experiences in Operating a Collaboratory: The Protein Data Bank...

www.pdb.org • [email protected]

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

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

http://www.ncbi.nlm.nih.gov/




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





um

ber

of

rele

ased

en

trie

s

Year





1970’s• 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)




www.pdb.org • [email protected] New Biology

CHAD





1980’s

• 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





1990’s • 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





Who does what?

• Rutgers– Data in: standards, validation, annotation

• UCSD/SDSC– Data out: search engine, Web site, data

distribution





Communication

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





Retreats

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





VTC’s

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





2000’s

• Continued growth in structure studies

• Structural genomics takes off

• RCSB PDB contract renewed

•

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

• Release of new database and website

BMRB joins RCSB





The PDB is Global





Worldwide Protein Data Bankwww.wwpdb.org





Mission

Maintain a single archive of macromolecular

structural data that is freely and openly available to

the global community





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





Guidelines and Responsibilities

• All members issue PDB ID’s 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





Future

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





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





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?




“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.”

Structural Genomics

From the NIH Request for Proposals for Structure Genomics Centers:

“The next step beyond the human genome project”

www.pdb.org • [email protected] - Structures (Sep-2005 1246 images)


Community

• Depositors– Different methods: X-ray, NMR, cryo-EM

• Users– Specialists (structural biologists)– Generalists– Educators– Students– Lay community


Active Outreach

• Electronic

• Meetings

• Publications

• One on one

• Many workshops


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


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


Acknowledgements

Operated by two members of the RCSB:

Supported by:

NIGMS

The RCSB PDB is a member of the

Www.pdb.org [email protected] Real World Experiences in Operating a Collaboratory: The Protein Data Bank...

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