Protein Data Bank (file format)
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| pdb | |
|---|---|
| File extension: | .pdb, .ent, .brk |
| Type of format: | chemical file format |
Please Take Over This Page and Apply to be Editor-In-Chief for this topic: There can be one or more than one Editor-In-Chief. You may also apply to be an Associate Editor-In-Chief of one of the subtopics below. Please mail us [1] to indicate your interest in serving either as an Editor-In-Chief of the entire topic or as an Associate Editor-In-Chief for a subtopic. Please be sure to attach your CV and or biographical sketch. The Protein Data Bank (pdb) file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank. As such, it contains atom position information and sequence information along with information about the researchers who defined the structure and a citation. There may also be optional remarks that are pertinent to understanding the information contained in the file.
Through the years the file format has undergone many changes and revisions. Its original format was dictated by the width of computer punch cards.
- PDB Format Guide - Prepared by the PDB Staff at BNL 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.
This legacy format has caused many problems with the format, and consequently the PDB has three distinct 'clean-up' projects;
- The Molecular Modeling DataBase (MMDB) from NCBI
- The Macromolecular Structure Database from the European Bioinformatics Institute
- The Data Uniformity Project from PDB
See also
- Chemical file format
- ScientificPython — provides an interface for Python
Acknowledgement and Attribution Regarding Sources of Content
Some of the initial content on this page may be incorporated in part from copyleft sources in the public domain including wikis such as Wikipedia and AskDrWiki. Drug information for patients came from the The National Library of Medicine. Infectious disease information may have come from the Centers for Disease Control (CDC). Differential Diagnoses are drawn from clinicians as well as an amalgamation of 3 sources: 1.The Disease Database; 2. Kahan, Scott, Smith, Ellen G. In A Page: Signs and Symptoms. Malden, Massachusetts: Blackwell Publishing, 2004:3; 3. Sailer, Christian, Wasner, Susanne. Differential Diagnosis Pocket. Hermosa Beach, CA: Borm Bruckmeir Publishing LLC, 2002:7 .
