Post on 12-Jan-2016
description
The Protein Data Bank:Evolution of a key resource in
biology
Helen M. Berman
September 9, 2010
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
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 181 662-666; Hemoglobin: Perutz (1962) Proc. R. Soc. A265, 161-187; Lysozyme: Blake, Koenig, Mair, North, Phillips, Sarma (1965) Nature 206 757; Ribonuclease: Kartha, Bello, Harker (1967) Nature 213, 862-865; Wyckoff, Hardman, Allewell, Inagami, Johnson, Richards (1967) J. Biol. Chem. 242, 3753-3757.
PDB Depositors
RCSB PDB173,416,704data downloads
PDBe32,344,547data downloads
PDBj14,053,071data downloads
PDB AccessPDB FTP & RSYNC Traffic (July 2009 – June 2010)
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
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
PDB History
wwPDB
Formalization of current working practice
MOU signed July 1, 2003
Announced in Nature Structural Biology November 21, 2003
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
Community involvement at every step
Formation of the resource Guidelines for deposition Standards for the data Global cooperation
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
Wellcome Trust, EU, CCP4, BBSRC, MRC, EMBL
NLM
BIRD-JST, MEXT
NSF, NIGMS, DOE, NLM, NCI, NINDS, NIDDK