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PDBWiki
PDBWiki was a wiki that functioned as a user-contributed database of protein structure annotations, listing all the protein structures available in the Protein Data Bank (PDB). It ran on the MediaWiki wiki application from 2007 to 2013. The website went offline in 2014 and there has not been any way to subsequently access the information that was contributed. PDBWiki contained 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 Bank (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-accessi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wiki
A wiki ( ) is an online hypertext publication collaboratively edited and managed by its own audience, using a web browser. A typical wiki contains multiple pages for the subjects or scope of the project, and could be either open to the public or limited to use within an organization for maintaining its internal knowledge base. Wikis are enabled by wiki software, otherwise known as wiki engines. A wiki engine, being a form of a content management system, differs from other web-based systems such as blog software, in that the content is created without any defined owner or leader, and wikis have little inherent structure, allowing structure to emerge according to the needs of the users. Wiki engines usually allow content to be written using a simplified markup language and sometimes edited with the help of a rich-text editor. There are dozens of different wiki engines in use, both standalone and part of other software, such as bug tracking systems. Some wiki engines are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spans formal techniques and practical considerations, including data modeling, efficient data representation and storage, query languages, security and privacy of sensitive data, and distributed computing issues, including supporting concurrent access and fault tolerance. A database management system (DBMS) is the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS software additionally encompasses the core facilities provided to administer the database. The sum total of the database, the DBMS and the associated applications can be referred to as a database system. Often the term "database" is also used loosely to refer to any of the DBMS, the database system or an appli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a ''residue'' indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This is t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. History Two force ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MediaWiki
MediaWiki is a free and open-source wiki software. It is used on Wikipedia and almost all other Wikimedia websites, including Wiktionary, Wikimedia Commons and Wikidata; these sites define a large part of the requirement set for MediaWiki. It was developed for use on Wikipedia in 2002, and given the name "MediaWiki" in 2003. MediaWiki was originally developed by Magnus Manske and improved by Lee Daniel Crocker. Magnus Manske's announcement of "PHP Wikipedia", wikipedia-l, August 24, 2001 Its development has since then been coordinated by the Wikimedia Foundation. MediaWiki is written in the PHP programming language and stores all text content into a database. The software is optimized to efficiently handle large projects, which can have terabytes of content and hundreds of thousands of views per second. Because Wikipedia is one of the world's largest websites, achieving scalability through multiple layers of caching and database replication has been a major concern for de ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wiki Application
Wiki software (also known as a wiki engine or a wiki application), is collaborative software that runs a wiki, which allows the users to create and collaboratively edit pages or entries via a web browser. A wiki system is usually a web application that runs on one or more web servers. The content, including previous revisions, is usually stored in either a file system or a database. Wikis are a type of web content management system, and the most commonly supported off-the-shelf software that web hosting facilities offer. There are dozens of actively maintained wiki engines. They vary in the platforms they run on, the programming language they were developed in, whether they are open-source or proprietary, their support for natural language characters and conventions, and their assumptions about technical versus social control of editing. History The first generally recognized "wiki" application, WikiWikiWeb, was created by American computer programmer Ward Cunningham in 199 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Archive
An archive is an accumulation of historical records or materials – in any medium – or the physical facility in which 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 that person or organization. Professional archivists and historians generally understand archives to be records that have been naturally and necessarily generated as a product of regular legal, commercial, administrative, or social activities. They have been metaphorically defined as "the secretions of an organism", and are distinguished from documents that have been consciously written or created to communicate a particular message to posterity. In general, archives consist of records that have been selected for permanent or long-term preservation on grounds of their enduring cultural, historical, or evidentiary value. Archival records are normally unpublished and almost alway ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
KOBIC
The Korean Bioinformation Center (KOBIC) is the Korean national research centre in bioinformatics, based in Daejeon, South Korea. The centre is comparable to the National Center for Biotechnology Information (NCBI) in the United States and the European Bioinformatics Institute (EBI) in Europe and plays a key role in various areas such as genomics, proteomics, systems biology, and personalized medicine. The research centre was originally established as the National Genome Information Center (NGIC) in 2001. It was designated as the National Center for Registration of Research Results in 2003 and gained its current name in 2006 by the NGIC director Jong Bhak who passed a bill to establish the national center for bioresource, biodiversity, and bioinformation. Prof. Jong Bhak coined the name KOGIC in 2005 and the formalization of the name was carried out by the vice prime minister Prof. Woosik Kim in 2006. KOBIC was designated as the National Center for Biological Research Resource In ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteopedia
Proteopedia is a wiki, 3D encyclopedia of proteins and other molecules. The site contains a page for every entry in the Protein Data Bank (>130,000 pages), 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 that highlights functional sites and ligands. It employs a scene-authoring tool so that users do not have to learn JSmol script language to create customized molecular scenes. Custom scenes are easily attached to "green links" in descriptive text that display those scenes in JSmol. A web browser is all that is needed to access the site and the 3D information; no viewers are required to be installed. Proteopedia was the winner of the 2010 award for the best website by '' The Scientist'' magazine. Legal aspects Licensing terms All user-added content is free and covered by the GNU Free Documentation License. Proteopedia is hosted at the Israel Structural Proteomics Center at ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
WikiProject Molecular And Cellular Biology
A WikiProject, or Wikiproject, is a Wikimedia movement affinity group for contributors with shared goals. WikiProjects are prevalent within the largest wiki, Wikipedia, and exist to varying degrees within sister projects such as Wiktionary, Wikiquote, Wikidata, and Wikisource. They also exist in different languages, and translation of articles is a form of their collaboration. During the COVID-19 pandemic, CBS News noted the role of Wikipedia's WikiProject Medicine in maintaining the accuracy of articles related to the disease. Another WikiProject that has drawn attention is WikiProject Women Scientists, which was profiled by '' Smithsonian'' for its efforts to improve coverage of women scientists which the profile noted had "helped increase the number of female scientists on Wikipedia from around 1,600 to over 5,000". On Wikipedia Some Wikipedia WikiProjects are substantial enough to engage in cooperative activities with outside organizations relevant to the field at issue. For ex ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Databases
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures. Biological databases can be classified by the kind of data they collect (see below). Broadly, there are molecular databases (for sequences, molecules, etc.), functional databases (for physiology, enzyme activities, phenotypes, ecology etc), taxonomic databases (for species and other taxonomic ranks), images and other media, or specimens (for museum collections etc.) Databases are important tools in assisting scientists to analyze and explain ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
