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

4. Number of released entries Year

5. 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)

7. CHAD Nature New Biology

8. 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

9. 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

11. Who does what? • Rutgers • Data in: standards, validation, annotation • UCSD/SDSC • Data out: search engine, Web site, data distribution

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

17. VTC’s • Two formal ones per week • Ad hoc when there are issues to discuss

18. 2000’s • 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

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

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 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

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. NIGMS Acknowledgements Operated by two members of the RCSB: The RCSB PDB is a member of the Supported by: