PDBWiki
Encyclopedia
PDBWiki is a wiki
that functions as a user-contributed database
of protein structure
annotations, listing all the protein structures currently available in the Protein Data Bank
(PDB). It runs on the MediaWiki
wiki application.
Currently PDBWiki contains details of more than 50,000 protein structures and over 50 'user-contributed' annotations, making it a significant resource for the structural biology community.
(PDB) is the central archive
of experimentally solved biomolecular structures. However, the PDB only allows data retrieval and does not provide functionality for collaboration or user feedback. In contrast, PDBWiki allows for sharing expert knowledge about structures deposited in the PDB. It provides tools for discussing and annotating proteins in a collaborative way. The goal is to create a central and freely-accessible repository of user-contributed information that will be useful for anyone working with PDB structures. As such PDBWiki can be considered a part of a wider effort in community-based biological databases curation.
.
Wiki
A wiki is a website that allows the creation and editing of any number of interlinked web pages via a web browser using a simplified markup language or a WYSIWYG text editor. Wikis are typically powered by wiki software and are often used collaboratively by multiple users. Examples include...
that functions as a user-contributed database
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
of protein structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
annotations, listing all the protein structures currently available in the Protein Data Bank
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
(PDB). It runs on the MediaWiki
MediaWiki
MediaWiki is a popular free web-based wiki software application. Developed by the Wikimedia Foundation, it is used to run all of its projects, including Wikipedia, Wiktionary and Wikinews. Numerous other wikis around the world also use it to power their websites...
wiki application.
Currently PDBWiki contains details of more than 50,000 protein structures and over 50 'user-contributed' annotations, making it a significant resource for the structural biology community.
Motivation
The Protein Data BankProtein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
(PDB) is the central archive
Archive
An archive is a collection of historical records, or the physical place they are located. Archives contain primary source documents that have accumulated over the course of an individual or organization's lifetime, and are kept to show the function of an organization...
of experimentally solved biomolecular structures. However, the PDB only allows data retrieval and does not provide functionality for collaboration or user feedback. In contrast, PDBWiki allows for sharing expert knowledge about structures deposited in the PDB. It provides tools for discussing and annotating proteins in a collaborative way. The goal is to create a central and freely-accessible repository of user-contributed information that will be useful for anyone working with PDB structures. As such PDBWiki can be considered a part of a wider effort in community-based biological databases curation.
About
PDBWiki was developed as part of the BioWiki initiative, and was entered into the third International Openfree Bioinformation Contents Competition organised by BiO.CC, a biological information website operated by KOBICKOBIC
KOBIC stands for the Korean Bioinformation Center. It is comparable to the US NCBI in America and EBI in Europe.The Korean Bioinformation Center was originally established as NGIC in 2001 in Korea...
.
See also
- ProteopediaProteopediaProteopedia is a wiki, 3D encyclopedia of proteins and other molecules..The site contains a page for every entry in the Protein Data Bank , as well as pages that are more descriptive of protein structures in general such as acetylcholinesterase, hemoglobin, and the photosystem II with a Jmol view...
- The Molecular and Cellular Biology 'WikiProject'.
External links
- The PDBWiki homepage
- About PDBWiki
- The Worldwide Protein Data Bank