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EM Data Bank
The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located. , the resource contained over 2,600 entries with a mean resolution of 15Å. Deposition of data was originally via the EMdep deposition interface, but since 2016 deposition of data has been incorporated into the wwPDB OneDep interface. Under the NIH Unified Data Resource for CryoEM, the Research Collaboration for Structural Biology (RCSB) also acts as a deposition, data processing and distribution center for EMDB data, while the National Center for Macromolecular Imaging (NCMI) is a collaborative partner in providing services and tools concerning the EMDB. EM Data Bank also provides the EMsearch search tool and data can also be queried at RCSB, EM ... [...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] |
CryoEM
Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample solution is applied to a grid-mesh and plunge-frozen in liquid ethane or a mixture of liquid ethane and propane. While development of the technique began in the 1970s, recent advances in detector technology and software algorithms have allowed for the determination of biomolecular structures at near-atomic resolution. This has attracted wide attention to the approach as an alternative to X-ray crystallography or NMR spectroscopy for macromolecular structure determination without the need for crystallization. In 2017, the Nobel Prize in Chemistry was awarded to Jacques Dubochet, Joachim Frank, and Richard Henderson "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution." ''Nature M ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
European Bioinformatics Institute
The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics. Additionally, the EMBL-EBI hosts training programs that teach scientists the fundamentals of the work with biological data and promote the plethora of bioinformatic tools available for their research, both EMBL-EBI and non-EMBL-EBI-based. Bioinformatic services One of the roles of the EMBL-EBI is to index and maintain biological data in a set of databases, including E ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BMC Bioinform
''BMC Bioinformatics'' is a peer-reviewed open access scientific journal covering bioinformatics and computational biology published by BioMed Central. It was established in 2000, and has been one of the fastest growing and most successful journals in the '' BMC Series'' of journals, publishing 1,000 articles in its first five years. Abstracting and indexing The journal is abstracted and indexed in: According to the ''Journal Citation Reports'', the journal has a 2020 impact factor The impact factor (IF) or journal impact factor (JIF) of an academic journal is a scientometric index calculated by Clarivate that reflects the yearly mean number of citations of articles published in the last two years in a given journal, as ... of 3.169. References External links *{{Official website, http://www.biomedcentral.com/bmcbioinformatics/ BioMed Central academic journals Bioinformatics and computational biology journals Creative Commons Attribution-licensed journals Public ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Worldwide Protein Data Bank
The Worldwide Protein Data Bank, wwPDB, is an organization that maintains the archive of macromolecular structure. Its mission is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. The organization has four members: *Research Collaboratory for Structural Bioinformatics Protein Database (RCSB PDB) *Protein Data Bank in Europe (PDBe) *Protein Data Bank Japan (PDBj) *Biological Magnetic Resonance Data Bank (BMRB) The wwPDB was founded in 2003 by RCSB PDB (USA), PDBe (Europe) and PDBj (Japan). In 2006 BMRB (USA) joined the wwPDB. Each member's site can accept structural data and process the data. The processed data is sent to the "archive keeper". The RCSB PDB presently acts as the "archive keeper". This ensures that there is only one version of the data which is identical for all users. The modified database is then made available to the other wwPDB members, each of whom makes the res ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rcsb
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 forces c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RCSB
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 forces c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
EMBL-EBI
The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics. Additionally, the EMBL-EBI hosts training programs that teach scientists the fundamentals of the work with biological data and promote the plethora of bioinformatic tools available for their research, both EMBL-EBI and non-EMBL-EBI-based. Bioinformatic services One of the roles of the EMBL-EBI is to index and maintain biological data in a set of databases, including ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
The Scripps Research Institute
Scripps Research, previously known as The Scripps Research Institute (TSRI), is a nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California, the institute has over 170 laboratories employing 2,100 scientists, technicians, graduate students, and administrative and other staff, making it the largest private, non-profit biomedical research organization in the United States and among the largest in the world. The institute holds over 1,100 patents, has produced 11 FDA-approved therapeutics, and has generated over 50 spin-off companies. According to the 2017 Nature Innovation Index, Scripps Research is the #1 most influential research institution in the world. The Scripps Research graduate program is ranked 9th nationally in the biological sciences, 6th for organic chemistry, and 6th for biochemistry. In 2022, their Jupiter, FL campus became a part of the University of Florida. Jupiter-based ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cryo-Electron Microscopy
Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample solution is applied to a grid-mesh and plunge-frozen in liquid ethane or a mixture of liquid ethane and propane. While development of the technique began in the 1970s, recent advances in detector technology and software algorithms have allowed for the determination of biomolecular structures at near-atomic resolution. This has attracted wide attention to the approach as an alternative to X-ray crystallography or NMR spectroscopy for macromolecular structure determination without the need for crystallization. In 2017, the Nobel Prize in Chemistry was awarded to Jacques Dubochet, Joachim Frank, and Richard Henderson "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution." ''Nature M ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Colocalization Benchmark Source
The Colocalization Benchmark Source (CBS) is a free collection of downloadable images to test and validate the degree of colocalization of markers in any fluorescence microscopy studies. Colocalization is a visual phenomenon when two molecules of interest are associated with the same structures in the cells and potentially share common functional characteristics. CBS provides researchers with reference tools to verify the results of quantitative colocalization measurements. It serves as a specialised bioimage informatics database of computer-simulated images with exactly known (pre-defined) values of colocalization. They were created using image simulation algorithm. These benchmark images can be downloaded as sets as well as separately. By calculating and comparing the values of coefficients on their images versus benchmark images, researchers can validate the results of quantitative colocalization studies. The use of CBS images was described in a number of studies.Zinchuk V et al ... [...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] |
