|
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. Further, 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-based and not so. Bioinformatic services One of the roles of the EMBL-EBI is to index and maintain biological data in a set of databases, including Ensembl (housing whole genome sequence data), UniProt (protein sequence and annotation database) and Protein Data Bank (protein and nucleic acid tertiary structure database). A variety of online services and tools is provided, such as Basic Local Alignment Search Tool (BLAST) or Clustal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wellcome Genome Campus
The Wellcome Genome Campus is a scientific research campus built in the grounds of Hinxton Hall, Hinxton in Cambridgeshire, England. Campus The Campus is home to some institutes and organisations in genomics and computational biology. The Campus is part of the Wellcome Trust, a global charitable foundation that exists to improve health, and houses the Wellcome Sanger Institute, the European Bioinformatics Institute (EBI), the bioinformatics outstation of the European Molecular Biology Laboratory (EMBL), and a number of biotech companies whose UK offices are located in the BioData Innovation Centre acting as an incubator for businesses of all sizes. In 2020, the South Cambridgeshire District Council granted outline planning permission for an expansion of the Campus. The expansion will increase the overall Campus grounds from 125 acres to 440 acres. The first buildings are expected to be completed in 2026. Activities At the Campus, genome and biodata research takes place. The C ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ProbCons
In bioinformatics and proteomics, ProbCons is an open source software for probabilistic consistency-based multiple alignment of amino acid sequences. It is one of the most efficient protein multiple sequence alignment programs, since it has repeatedly demonstrated a statistically significant advantage in accuracy over similar tools, including Clustal and MAFFT. Algorithm The following describes the basic outline of the ProbCons algorithm. Step 1: Reliability of an alignment edge For every pair of sequences compute the probability that letters x_i and y_i are paired in a^* an alignment that is generated by the model. \begin P(x_i \sim y_i, x,y) \ \overset& \ \Pr x,y\\ pt =& \ \sum_ \Pr x,y\\ pt =& \ \sum_ \mathbf\ \Pr x,y\end (Where \mathbf\ is equal to 1 if x_i and y_i are in the alignment and 0 otherwise.) Step 2: Maximum expected accuracy The accuracy of an alignment a^* with respect to another alignment a is defined as the number of common aligned pairs divided by the le ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
AlphaFold
AlphaFold is an artificial intelligence (AI) program developed by DeepMind, a subsidiary of Alphabet, which performs predictions of protein structure. It is designed using deep learning techniques. AlphaFold 1 (2018) placed first in the overall rankings of the 13th Critical Assessment of Structure Prediction (CASP) in December 2018. It was particularly successful at predicting the most accurate structures for targets rated as most difficult by the competition organizers, where no existing template structures were available from proteins with partially similar sequences. AlphaFold 2 (2020) repeated this placement in the CASP14 competition in November 2020. It achieved a level of accuracy much higher than any other entry. It scored above 90 on CASP's global distance test (GDT) for approximately two-thirds of the proteins, a test measuring the similarity between a computationally predicted structure and the experimentally determined structure, where 100 represents a complete matc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Google DeepMind
DeepMind Technologies Limited, trading as Google DeepMind or simply DeepMind, is a British–American artificial intelligence research laboratory which serves as a subsidiary of Alphabet Inc. Founded in the UK in 2010, it was acquired by Google in 2014 and merged with Google AI's Google Brain division to become Google DeepMind in April 2023. The company is headquartered in London, with research centres in the United States, Canada, France, Germany, and Switzerland. DeepMind introduced neural Turing machines (neural networks that can access external memory like a conventional Turing machine), resulting in a computer that loosely resembles short-term memory in the human brain. DeepMind has created neural network models to play video games and board games. It made headlines in 2016 after its AlphaGo program beat a human professional Go player Lee Sedol, a world champion, in a five-game match, which was the subject of a documentary film. A more general program, AlphaZero, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Information Resource
The Protein Information Resource (PIR), located at Georgetown University Medical Center, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies. It contains protein sequences databases History PIR was established in 1984 by the National Biomedical Research Foundation as a resource to assist researchers and customers in the identification and interpretation of protein sequence information. Prior to that, the foundation compiled the first comprehensive collection of macromolecular sequences in the Atlas of Protein Sequence and Structure, published from 1964 to 1974 under the editorship of Margaret Dayhoff. Dayhoff and her research group pioneered in the development of computer methods for the comparison of protein sequences, for the detection of distantly related sequences and duplications within sequences, and for the inference of evolutionary histories from alignments of protein sequences. Winona Barker and Robert Ledle ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Swiss Institute Of Bioinformatics
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland. The institute was established on 30 March 1998 and its mission is to provide core bioinformatics resources to the national and international life science research community in fields such as genomics, proteomics and systems biology as well as to lead and coordinate the field of bioinformatics in Switzerland. In particular, it promotes research, develops databanks and computer technologies, and is involved in teaching and service activities. History The institute was originally created to provide a framework for stable long-term funding for both the Swiss-Prot database and the Swiss EMBnet node. Swiss-Prot in particular went through a major funding crisis in 1996, which led the leaders of the five research groups active in bioinformatics in Geneva and Lausanne, Ron Appel, Amos Bairoch, Philipp Bucher, Victor Jongeneel and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UniProt
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, USA. The UniProt consortium The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy (Expert Protein Analysis System) servers that are a central resource for proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation (NBRF) at the George ... [...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 A macromolecule is a "molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." Polymers are physi ... structural data that is freely and publicly available to the global community. The organization has five 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) * Electron Microscopy Data Bank (EMDB). The wwPDB was founded in 2003 by RCSB PDB (USA), PDBe (Europe) and PDBj (Japan). In 2006 BMRB (USA) joined the wwPDB. EMDB (UK) joined in 2021. Each member's site can accept structural da ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PDBe-KB
Protein Data Bank in Europe – Knowledge Base (PDBe-KB) is a community-driven, open-access, integrated resource whose mission is to place macromolecular structure data in their biological context and to make them accessible to the scientific community in order to support fundamental and translational research and education. It is part of the European Bioinformatics Institute (EMBL-EBI), based at the Wellcome Genome Campus, Hinxton Hinxton is a village in South Cambridgeshire, England. The River Cam runs through the village, as does the Cambridge to Liverpool Street station, Liverpool Street railway, though the village has no station. Hinxton parish's southern boundarie ..., Cambridgeshire, England. References Medical databases Science and technology in Cambridgeshire South Cambridgeshire District {{biochem-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nuclear Magnetic Resonance Spectroscopy
Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a Spectroscopy, spectroscopic technique based on re-orientation of Atomic nucleus, atomic nuclei with non-zero nuclear spins in an external magnetic field. This re-orientation occurs with absorption of electromagnetic radiation in the radio frequency region from roughly 4 to 900 MHz, which depends on the Isotope, isotopic nature of the nucleus and increases proportionally to the strength of the external magnetic field. Notably, the resonance frequency of each NMR-active nucleus depends on its chemical environment. As a result, NMR spectra provide information about individual functional groups present in the sample, as well as about connections between nearby nuclei in the same molecule. As the NMR spectra are unique or highly characteristic to individual compounds and functional groups, NMR spectroscopy is one of the most important methods to identify ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
X-ray Crystallography
X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract in specific directions. By measuring the angles and intensities of the X-ray diffraction, a crystallography, crystallographer can produce a three-dimensional picture of the density of electrons within the crystal and the positions of the atoms, as well as their chemical bonds, crystallographic disorder, and other information. X-ray crystallography has been fundamental in the development of many scientific fields. In its first decades of use, this method determined the size of atoms, the lengths and types of chemical bonds, and the atomic-scale differences between various materials, especially minerals and alloys. The method has also revealed the structure and function of many biological molecules, including vitamins, drugs, proteins and nucleic acids such as DNA. X-ray crystall ... [...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, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, Nuclear magnetic resonance spectroscopy of proteins, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert Biocuration, biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organizations (PDBe, PDBj, RCSB PDB, and BMRB). 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
