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CAMEO3D
Continuous Automated Model EvaluatiOn (CAMEO) is a community-wide project to continuously evaluate the accuracy and reliability of protein structure prediction servers in a fully automated manner. CAMEO is a continuous and fully automated complement to the bi-annual CASP experiment. Currently, CAMEO evaluates predictions for predicted three-dimensional protein structures (3D), ligand binding site predictions in proteins (LB), and model quality estimation tools (QE). Workflow CAMEO performs blind assessment of protein structure prediction techniques based on the weekly releases of newly determined experimental structures by the Protein Databank (PDB). The amino acid sequences of soon to be released protein structures are submitted to the participating web-servers. The web-servers return their predictions to CAMEO, and predictions received before the experimental structures have been released are included in the assessment of prediction accuracy. In contrast to the CASP experimen ... [...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] |
Protein Model Portal
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure Prediction Software
This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ''ab initio'' methods, secondary structure prediction, and transmembrane helix and signal peptide prediction. Software list Below is a list which separates programs according to the method used for structure prediction. Homology modeling Threading/fold recognition ''Ab initio'' structure prediction Secondary structure prediction Detailed list of programs can be found at List of protein secondary structure prediction programs See also *List of protein secondary structure prediction programs *Comparison of nucleic acid simulation software * List of software for molecular mechanics modeling * Molecular design software *Protein design Protein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein fun ... [...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] |
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] |
Biozentrum, University Of Basel
The Biozentrum of the University of Basel specializes in basic molecular and biomedical research and teaching. Research includes the areas of cell growth and development, infection biology, neurobiology, structural biology and biophysics, and computational and systems biology. With 500 employees, the Biozentrum is the largest department at the University of Basel's Faculty of Science. It is home to 30 research groups with scientists from more than 40 nations. History In 1971, at the time when the Biozentrum was founded, the concept of developing an interdisciplinary biological research facility was unique in Europe. Scientists from academy and industry as well as representatives of the Canton of Basel-Stadt promoted the Biozentrum's development. In the winter semester 1972/73 the first students enrolled for the new "Biology II" curriculum. It encompassed a two-year foundation course in mathematics, physics and chemistry as well as a cycle of block courses – a new teac ... [...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 a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure Initiative
The Protein Structure Initiative (PSI) was a USA based project that aimed at accelerating discovery in structural genomics and contribute to understanding biological function. Funded by the U.S. National Institute of General Medical Sciences (NIGMS) between 2000 and 2015, its aim was to reduce the cost and time required to determine three-dimensional protein structures and to develop techniques for solving challenging problems in structural biology, including membrane proteins. Over a dozen research centers have been supported by the PSI for work in building and maintaining high-throughput structural genomics pipelines, developing computational protein structure prediction methods, organizing and disseminating information generated by the PSI, and applying high-throughput structure determination to study a broad range of important biological and biomedical problems. The project has been organized into three separate phases. The first phase of the Protein Structure Initiative (PSI- ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Journal Of Structural And Functional Genomics
A journal, from the Old French ''journal'' (meaning "daily"), may refer to: *Bullet journal, a method of personal organization *Diary, a record of what happened over the course of a day or other period *Daybook, also known as a general journal, a daily record of financial transactions *Logbook, a record of events important to the operation of a vehicle, facility, or otherwise *Record (other) *Transaction log, a chronological record of data processing *Travel journal In publishing, ''journal'' can refer to various periodicals or serials: *Academic journal, an academic or scholarly periodical **Scientific journal, an academic journal focusing on science **Medical journal, an academic journal focusing on medicine **Law review, a professional journal focusing on legal interpretation *Magazine, non-academic or scholarly periodicals in general **Trade magazine, a magazine of interest to those of a particular profession or trade **Literary magazine, a magazine devoted to literat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics (journal)
''Bioinformatics'' (sometimes called ''Bioinformatics Oxford journal'') is a biweekly peer-reviewed scientific journal covering research and software in bioinformatics and computational biology. It is the official journal of the International Society for Computational Biology (ISCB), together with ''PLOS Computational Biology''. Authors can pay extra for open access and are allowed to self-archive after 1 year. The journal was established as ''Computer Applications in the Biosciences'' (''CABIOS'') in 1985. The founding editor-in-chief was Robert J. Beynon. In 1998, the journal obtained its current name and established an online version of the journal. It is published by Oxford University Press and, as of 2014, the editors-in-chief are Alfonso Valencia and Janet Kelso. Previous editors include Chris Sander, Gary Stormo, Christos Ouzounis, Martin Bishop, and Alex Bateman. In 2014, these five editors were appointed the first Honorary Editors of ''Bioinformatics''. According to the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database (journal)
''Database: The Journal of Biological Databases and Curation'' is an online peer-reviewed open access scientific journal that covers research on databases and biocuration. The journal was established in 2009 with David Landsman as the editor-in-chief. DATABASE is the official journal of the International Society for Biocuration. The journal has published the proceedings of the International Biocuration Conferences since 2009. Abstracting and indexing The journal is abstracted and indexed in MEDLINE/PubMed, Asian Science Citation Index, and Chemical Abstracts. 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 3.451. References External links * {{Authority control Biology journal ... [...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] |
