Protein Data Bank
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Protein Data Bank
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The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. This data, typically obtained by X-ray crystallography or NMR spectroscopy, is submitted by biologists and biochemists from around the world, is released into the public domain, and can be accessed for free.
Founded in 1971 by Brookhaven National Laboratory, management of the Protein Data Bank was transferred in 1998 to members of the Research Collaboratory for Structural Bioinformatics (RCSB).
The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.
When the PDB was originally founded it contained just 7 protein structures. Since then it has undergone an approximate exponential growth in the number of structures, which does not show any sign of falling off.
The growth rate of the PDB has been the subject of fairly extensive analysis.
As of 26 September, 2006, the database contained 39,051 released atomic coordinate entries (or "structures"), 35,767 of that proteins, the rest being nucleic acids, nucleic acid-protein complexes, and a few other molecules. About 5,000 new structures are released each year. Data are stored in the mmCIF format specifically developed for the purpose.
Note that the database stores information about the exact location of all atoms in a large biomolecule (although, usually without the hydrogen atoms, as their positions are more of a statistical estimate); if one is only interested in sequence data, i.e. the list of amino acids making up a particular protein or the list of nucleotides making up a particular nucleic acid, the much larger databases from Swiss-Prot and the International Nucleotide Sequence Database Collaboration should be used.
|Proteins||Nucleic Acids||Protein/NA complexes||Other||Total|
Note that theoretical models are no longer accepted in the PDB.
22461 structures in the PDB have a structure factor file. 3138 structures in the PDB have an NMR restraint file.
The current breakdown of holdings is updated weekly.
Through the years the PDB file format has undergone many, many changes and revisions. Its original format was dictated by the width of computer punch cards.
- PDB Format Guide Version 2.3- Prepared by the wwPDB. The PDB format specification can be found here, and it is vital that you read this before looking at the raw data.
- Recently PDB provides a representation of PDB data in XML format, PDBML format.
- ftp.rcsb.org The raw data can be downloaded from here.
- PDB format files can be downloaded using HTTP with URLs like this: http://www.pdb.org/pdb/files/4hhb.pdb.gz
- PDBML (XML) files can be downloaded using HTTP with URLs like this: http://www.pdb.org/pdb/files/4hhb.xml.gz
- ftp.ebi.ac.uk/pub/databases/rcsb/ Alternate download location for the PDB archive.
- www.pdb.org Statistics about the PDB can be found here.
This legacy format has caused many problems with the format, and consequently there are 'clean-up' projects;
The MMDB uses ASN.1 (and an XML conversion of this format). The wwPDB members RCSB PDB, MSD-EBI, and PDBj are working together to make the data uniform across the archive. Some believe this to be desirable; others argue that, without a universal repository of information (i.e., a common dictionary), it is not possible to draw comparisons.
Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. This should not be used as an identifier for biomolecules, since often several structures for the same molecule (in different environments or conformations) are contained in PDB with different PDB IDs.
If a biologist submits structure data for a protein or nucleic acid, wwPDB staff reviews and annotates the entry. The data are then automatically checked for plausibility. The source code for this validation software has been released for free. The main data base accepts only experimentally derived structures, and not theoretically predicted ones (see protein structure prediction).
Various funding agencies and scientific journals now require scientists to submit their structure data to PDB.
Viewing the data
The structural data can be used to visualize the biomolecules with appropriate software, such as VMD, RasMol, PyMOL, Jmol, MDL Chime, QuteMol, web browser VRML plugin or any web-based software designed to visualize and analyse the protein structures such as STING. A recent desktop software addition is Sirius. The RCSB PDB website also contains resources for education, structural genomics, and related software.
- H.M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980 PMID 14634627.
- H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000). PMID 10592235
- Bernstein FC, Koetzle TF, Williams GJ, Meyer Jr EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542. PMID 875032.
- Sussman, JL, Lin, D, Jiang, J, Manning, NO, Prilusky, J, Ritter, O & Abola, EE. Protein data bank (PDB): a database of 3D structural information of biological macromolecules. Acta Cryst 1998; D54:1078-1084. PMID 10089483.
- The Worldwide Protein Data Bank (wwPDB) — parent site to regional hosts (below)
- RCSB Protein Data Bank - home page
- MSD-EBI - home page
- Protein Data Bank Japan - home page
- ExPASy - Swiss-Prot and TrEMBL
- DNA Sequence Collaborator's Page International Nucleotide Sequence Database Collaboration
Links to enzyme database data
-  The best mapping is provided by Kim Henrick's group at EBI as part of the MSD SIFTS initiative.
-  PDB provide a mapping on their beta site, but it is at the whole PDB level not chain level.
-  Search at BRENDA enzyme database portal.
-  PDBSProtEC:
Molecular Graphic Visualisation Tools
- PyMOL — PyMol Home Page
- Sirius — Sirius Home Page
- RasMol — RasMol Home Page
- Swiss-PDB Viewer
- Jmol Viewer Open Source, Java based
- QuteMol — QuteMol Home Page Open Source, Win & Mac, high quality interactive molecule viewer
- StarBiochem java protein viewer with integrated search of protein databank
WikiDoc Research Resources for Protein Data Bank
|Articles on Protein Data Bank||Most recent articles on Protein Data Bank • Most cited articles on Protein Data Bank • Review articles on Protein Data Bank • Articles on Protein Data Bank in N Eng J Med, Lancet, BMJ|
|Media (Slides, Video, Images, MP3) on Protein Data Bank||Powerpoint slides on Protein Data Bank • Images of Protein Data Bank • Photos of Protein Data Bank • Podcasts & MP3s on Protein Data Bank • Videos on Protein Data Bank|
|Evidence Based Medicine Regarding Protein Data Bank||AND (Cochrane Database Syst Rev[http://worldselectshop.com/?id=9361 Cochrane Collaboration on Protein Data Bank • Bandolier on Protein Data Bank • TRIP on Protein Data Bank|
|Cost Effectiveness of Protein Data Bank||AND (Cost effectiveness)|
| group5 = Clinical Trials Involving Protein Data Bank | list5 = Ongoing Trials on Protein Data Bank at Clinical Trials.gov • Trial results on Protein Data Bank • Clinical Trials on Protein Data Bank at Google
| group6 = Guidelines / Policies / Government Resources (FDA/CDC) Regarding Protein Data Bank | list6 = US National Guidelines Clearinghouse on Protein Data Bank • NICE Guidance on Protein Data Bank • NHS PRODIGY Guidance • FDA on Protein Data Bank • CDC on Protein Data Bank
| group7 = Textbook Information on Protein Data Bank | list7 = Books and Textbook Information on Protein Data Bank
| group8 = Pharmacology Resources on Protein Data Bank | list8 = AND (Dose)}} Dosing of Protein Data Bank • AND (drug interactions)}} Drug interactions with Protein Data Bank • AND (side effects)}} Side effects of Protein Data Bank • AND (Allergy)}} Allergic reactions to Protein Data Bank • AND (overdose)}} Overdose information on Protein Data Bank • AND (carcinogenicity)}} Carcinogenicity information on Protein Data Bank • AND (pregnancy)}} Protein Data Bank in pregnancy • AND (pharmacokinetics)}} Pharmacokinetics of Protein Data Bank •
| group9 = Genetics, Pharmacogenomics, and Proteinomics of Protein Data Bank | list9 = AND (pharmacogenomics)}} Genetics of Protein Data Bank • AND (pharmacogenomics)}} Pharmacogenomics of Protein Data Bank • AND (proteomics)}} Proteomics of Protein Data Bank
| group11 = Commentary on Protein Data Bank | list11 = Blogs on Protein Data Bank
| group12 = Patient Resources on Protein Data Bank | list12 = Patient resources on Protein Data Bank • Discussion groups on Protein Data Bank • Patient Handouts on Protein Data Bank • Directions to Hospitals Treating Protein Data Bank • Risk calculators and risk factors for Protein Data Bank
| group13 = Healthcare Provider Resources on Protein Data Bank | list13 = Symptoms of Protein Data Bank • Causes & Risk Factors for Protein Data Bank • Diagnostic studies for Protein Data Bank • Treatment of Protein Data Bank
| group14 = Continuing Medical Education (CME) Programs on Protein Data Bank | list14 = CME Programs on Protein Data Bank
| group17 = Informatics Resources on Protein Data Bank | list17 = List of terms related to Protein Data Bank