1 / 12

The Protein Data Bank: Evolution of a key resource in biology

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)

jolene
Download Presentation

The Protein Data Bank: Evolution of a key resource in biology

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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 Myoglobin Hemoglobin Lysozyme Ribonuclease 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.

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

  5. PDB History

  6. PDB History

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

  8. 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

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

  10. Contributing factors for success • The sciencethat is being archived must be important enough for people to want to access results • The technologyfor 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

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

More Related