Protein structure database

See also: Sequence database

In biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way.

The Protein Data Bank

Main article: Protein Data Bank

The Protein Data Bank (PDB) was established in 1971 as the central archive of all experimentally determined protein structure data. Today the PDB is maintained by an international consortia collectively known as the Worldwide Protein Data Bank (wwPDB). The mission of the wwPDB is to maintain a single archive of macromolecular structural data that is freely and publicly available to the global community.

Protein structure databases

Because the PDB releases data into the public domain, the data has been used in various other protein structure databases.

Examples of protein structure databases include (in alphabetical order);

Database of Macromolecular Movements

describes the motions that occur in proteins and other macromolecules, particularly using movies [1]

JenaLib

the Jena Library of Biological Macromolecules [2] is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis.

MODBASE

a database of three-dimensional protein models calculated by comparative modeling [3]

PDBe

is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures, and a member of the Worldwide Protein Data Bank. [4]

OCA

a browser-database for protein structure/function [5] - The OCA integrates information from KEGG, OMIM, PDBselect, Pfam, PubMed, SCOP, SwissProt and others.

OPM

provides spatial positions of protein three-dimensional structures with respect to the lipid bilayer.

PDB Lite

derived from OCA, PDB Lite was provided to make it as easy as possible to find and view a macromolecule within the PDB [6]

PDBsum

provides an overview macromolecular structures in the PDB, giving schematic diagrams of the molecules in each structure and of the interactions between them [7]

PDBTM

the Protein Data Bank of Transmembrane Proteins [8] a selection of the PDB.

PDBWiki

a community annotated knowledge base of biological molecular structures [9]

Protein

the NIH protein database, a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB

Proteopedia

the collaborative, 3D encyclopedia of proteins and other molecules. A wiki that contains a page for every entry in the PDB (>50,000 pages), with a Jmol view that highlights functional sites and ligands. Offers an easy-to-use scene-authoring tool so you don't have to learn Jmol script language to create customized molecular scenes. Custom scenes are easily attached to "green links" in descriptive text that display those scenes in Jmol.

SCOP

the Structural Classification of Proteins [10] a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.

SWISS-MODEL Repository

a database of annotated protein models calculated by homology modeling [11]

TOPSAN

the Open Protein Structure Annotation Network [12] a wiki designed to collect, share and distribute information about protein three-dimensional structures.

Comparison

Protein structure database comparison table.

See also

• The External Links section of the Protein Data Bank article.