1. The Protein Data Bank: Evolution of a key resource in biology
Helen M. Berman
September 9, 2010

2. What is the Protein Data Bank?
Single international archive for all information about the structure of large biological molecules (>67,000 entries)
Archival database with hundreds of thousands of users who depend on the data
Used by structural biologists, computational biologists, biophysicists, biochemists, geneticists, cell biologists, molecular biologists, educators, students, general public

3. Early structures 1960s: Protein crystallography begins to take off
Emerging interest in protein folding
Use of computer graphics to represent structure
Nobel Prize awarded for the first 3D protein structures: myoglobin and hemoglobin
Lysozyme
Hemoglobin
Ribonuclease
Myoglobin
Myoglobin: Kendrew, Bodo, Dintzis, Parrish, Wyckoff, Phillips (1958) Nature ; Hemoglobin: Perutz (1962) Proc. R. Soc. A265, ; Lysozyme: Blake, Koenig, Mair, North, Phillips, Sarma (1965) Nature ; Ribonuclease: Kartha, Bello, Harker (1967) Nature 213, ; Wyckoff, Hardman, Allewell, Inagami, Johnson, Richards (1967) J. Biol. Chem. 242, 3

4. 4 4

5. PDB Depositors PDB Access PDB FTP & RSYNC Traffic
(July 2009 – June 2010)
RCSB PDB
173,416,704
data downloads
PDBe
32,344,547
data downloads
PDBj
14,053,071
data downloads 5

6. PDB History
1970s
Community discussions about a protein structure archive
Cold Spring Harbor meeting in protein crystallography
PDB established at Brookhaven (Oct 1971; 7 structures)
1980s
Number of structures increases as technology improves
Community discussions about requiring depositions
IUCr guidelines established
Number of structures deposited increases
show petition
iucr article
illustrate mmcif 6

7. PDB History 1990s mmCIF standard created Structural genomics begins
PDB moves to RCSB PDB
2000s
wwPDB formed
New methods for structure determination
Demand for new validation standards
show petition
iucr article
illustrate mmcif 7

8. wwPDB Formalization of current working practice
MOU signed July 1, 2003
Announced in Nature Structural Biology November 21, 2003

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

10. Community involvement at every step
Formation of the resource
Guidelines for deposition
Standards for the data
Global cooperation

11. Contributing factors for success
The science that is being archived must be important enough for people to want to access results
The technology for data archiving must be continually evaluated and changed as IT changes
The creation of an international organization recognizes the fact that science is global
Understanding sociological issues of both the data users and the data producers
Attribution of the work of data producers

12. 12 Wellcome Trust, EU, CCP4, BBSRC, MRC, EMBL BIRD-JST, MEXT NLM
NSF, NIGMS, DOE, NLM, NCI,
NINDS, NIDDK 12