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Critical Assessment Of Techniques For Protein Structure Prediction
Critical Assessment of Structure Prediction (CASP), sometimes called Critical Assessment of Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994. CASP provides research groups with an opportunity to objectively test their structure prediction methods and delivers an independent assessment of the state of the art in protein structure modeling to the research community and software users. Even though the primary goal of CASP is to help advance the methods of identifying protein three-dimensional structure from its amino acid sequence many view the experiment more as a “world championship” in this field of science. More than 100 research groups from all over the world participate in CASP on a regular basis and it is not uncommon for entire groups to suspend their other research for months while they focus on getting their servers ready for the experiment and on performing the detailed predic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure Prediction
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes). Starting in 1994, the performance of current methods is assessed biannually in the CASP experiment (Critical Assessment of Techniques for Protein Structure Prediction). A continuous evaluation of protein structure prediction web servers is performed by the community project CAMEO3D. Protein structure and terminology Proteins are chains of amino acids joined together by peptide bonds. Many conformations of this chain are possible due to the rotation of the main chain abou ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Critical Assessment Of Genome Interpretation
The Critical Assessment of Genome Interpretation (CAGI) is an annual bioinformatics competition focused on interpretation of genome variation. References {{bioinformatics-stub Bioinformatics ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Critical Assessment Of Function Annotation
The Critical Assessment of Functional Annotation (CAFA) is an experiment designed to provide a large-scale assessment of computational methods dedicated to predicting protein function. Different algorithms are evaluated by their ability to predict the Gene Ontology (GO) terms in the categories of Molecular Function, Biological Process, and Cellular Component. The experiment consists of two tracks: (i) the eukaryotic track, (ii) the prokaryotic track. In each track, a set of targets is provided by the organizers. Participants are expected to submit their predictions by the submission deadline, after which they are assessed according to a set of specific metrics. Motivation The genome of an organism may consist of hundreds to tens of thousands of genes, which encode for hundreds of thousands of different protein sequences. Due to the relatively low cost of genome sequencing, determining gene and protein sequences is fast and inexpensive. Thousands of species have been sequenced s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DeepMind
DeepMind Technologies is a British artificial intelligence subsidiary of Alphabet Inc. and research laboratory founded in 2010. DeepMind was List of mergers and acquisitions by Google, acquired by Google in 2014 and became a wholly owned subsidiary of Alphabet Inc., Alphabet Inc, after Google's restructuring in 2015. The company is based in London, with research centres in Canada, France, and the United States. DeepMind has created a neural network that learns how to play video games in a fashion similar to that of humans, as well as a Neural Turing machine, or a neural network that may be able to access an external memory like a conventional Turing machine, resulting in a computer that mimics the short-term memory of the human brain. DeepMind made headlines in 2016 after its AlphaGo program beat a human professional Go (game), Go player Lee Sedol, a world champion, in AlphaGo versus Lee Sedol, a five-game match, which was the subject of a documentary film. A more general progr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Artificial Intelligence
Artificial intelligence (AI) is intelligence—perceiving, synthesizing, and inferring information—demonstrated by machines, as opposed to intelligence displayed by animals and humans. Example tasks in which this is done include speech recognition, computer vision, translation between (natural) languages, as well as other mappings of inputs. The ''Oxford English Dictionary'' of Oxford University Press defines artificial intelligence as: the theory and development of computer systems able to perform tasks that normally require human intelligence, such as visual perception, speech recognition, decision-making, and translation between languages. AI applications include advanced web search engines (e.g., Google), recommendation systems (used by YouTube, Amazon and Netflix), understanding human speech (such as Siri and Alexa), self-driving cars (e.g., Tesla), automated decision-making and competing at the highest level in strategic game systems (such as chess and Go). ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
AlphaFold
AlphaFold is an artificial intelligence (AI) program developed by DeepMind, a subsidiary of Alphabet Inc., Alphabet, which performs Protein structure prediction, predictions of protein structure. The program is designed as a deep learning system. AlphaFold AI software has had two major versions. A team of researchers that used AlphaFold 1 (2018) placed first in the overall rankings of the 13th Critical Assessment of protein Structure Prediction (CASP) in December 2018. The program was particularly successful at predicting the most accurate structure for targets rated as the most difficult by the competition organisers, where no existing Threading (protein sequence), template structures were available from proteins with a partially similar sequence. A team that used AlphaFold 2 (2020) repeated the placement in the CASP competition in November 2020. The team achieved a level of accuracy much higher than any other group. It scored above 90 for around two-thirds of the proteins in C ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
EVA (benchmark)
EVA was a continuously running Benchmark (computing), benchmark project for assessing the quality and value of protein structure prediction and Protein structure prediction#Secondary structure, secondary structure prediction methods. Methods for predicting both secondary structure and tertiary structure - including homology modeling, protein threading, and contact order prediction - were compared to results from each week's newly solved protein structures deposited in the Protein Data Bank. The project aimed to determine the prediction accuracy that would be expected for non-expert users of common, publicly available prediction webservers; this is similar to the related LiveBench project and stands in contrast to the bi-yearly benchmark CASP, which aims to identify the maximum accuracy achievable by prediction experts. References * Rost B, Eyrich VA. (2001). EVA: large-scale analysis of secondary structure prediction. ''Proteins'' Suppl 5:192-9. * Eyrich VA, Marti-Renom MA, Przybyl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LiveBench
LiveBench is a continuously running benchmark project for assessing the quality of protein structure prediction and secondary structure prediction methods. LiveBench focuses mainly on homology modeling and protein threading but also includes secondary structure prediction, comparing publicly available webserver output to newly deposited protein structures in the Protein Data Bank. Like the EVA project and unlike the related CASP Critical Assessment of Structure Prediction (CASP), sometimes called Critical Assessment of Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994. CASP prov ... and CAFASP experiments, LiveBench is intended to study the accuracy of predictions that would be obtained by non-expert users of publicly available prediction methods. A major advantage of LiveBench and EVA over CASP projects, which run once every two years, is their comparatively large data set. Reference ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Function (biology)
In evolutionary biology, function is the reason some object or process occurred in a system that evolved through natural selection. That reason is typically that it achieves some result, such as that chlorophyll helps to capture the energy of sunlight in photosynthesis. Hence, the organism that contains it is more likely to survive and reproduce, in other words the function increases the organism's fitness. A characteristic that assists in evolution is called an adaptation; other characteristics may be non-functional spandrels, though these in turn may later be co-opted by evolution to serve new functions. In biology, function has been defined in many ways. In physiology, it is simply what an organ, tissue, cell or molecule does. In the philosophy of biology, talk of function inevitably suggests some kind of teleological purpose, even though natural selection operates without any goal for the future. All the same, biologists often use teleological language as a shorthand for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Domain
In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins. Background The concept of the domain was first proposed in 1973 by Wetlaufer aft ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intrinsically Disordered Proteins
In molecular biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs range from fully unstructured to partially structured and include random coil, molten globule-like aggregates, or flexible linkers in large multi-domain proteins. They are sometimes considered as a separate class of proteins along with globular, fibrous and membrane proteins. IDPs are a very large and functionally important class of proteins and their discovery has disproved the idea that three-dimensional structures of proteins must be fixed to accomplish their biological functions. For example, IDPs have been identified to participate in weak multivalent interactions that are highly cooperative and dynamic, lending them importance in DNA regulation and in cell signaling. Many IDPs can also adopt a fixed three-dimensional structure after bi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
