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RaptorX Software For Protein Modeling And Analysis
RaptorX is a software and web server for protein structure and function prediction that is free for non-commercial use. RaptorX is among the most popular methods for protein structure prediction. Like other remote homology recognition/protein threading techniques, RaptorX is able to regularly generate reliable protein models when the widely used BLAST, PSI-BLAST cannot. However, RaptorX is also significantly different from those profile-based methods (e.g., HHpred / HHsearch, HHPred and Phyre2) in that RaptorX excels at modeling of protein sequences without a large number of sequence homologs by exploiting structure information. RaptorX Server has been designed to ensure a user-friendly interface for users inexpert in protein structure prediction methods. Description The RaptorX project was started in 2008 and RaptorX Server was released to the public in 2011. Standard usage After pasting a protein sequence into the RaptorX submission form, a user will typically wait a coup ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
English Language
English is a West Germanic language of the Indo-European language family, with its earliest forms spoken by the inhabitants of early medieval England. It is named after the Angles, one of the ancient Germanic peoples that migrated to the island of Great Britain. Existing on a dialect continuum with Scots, and then closest related to the Low Saxon and Frisian languages, English is genealogically West Germanic. However, its vocabulary is also distinctively influenced by dialects of France (about 29% of Modern English words) and Latin (also about 29%), plus some grammar and a small amount of core vocabulary influenced by Old Norse (a North Germanic language). Speakers of English are called Anglophones. The earliest forms of English, collectively known as Old English, evolved from a group of West Germanic ( Ingvaeonic) dialects brought to Great Britain by Anglo-Saxon settlers in the 5th century and further mutated by Norse-speaking Viking settlers starting in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms ( SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable propertie ... [...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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteins (journal)
''Proteins: Structure, Function, and Bioinformatics'' is a monthly peer-reviewed scientific journal published by John Wiley & Sons, which was established in 1986 by Cyrus Levinthal. The journal covers research on all aspects protein biochemistry, including computation, function, structure, design, and genetics. The editor-in-chief is Nikolay Dokholyan ( Penn State College of Medicine). Publishing formats are original research reports, short communications, prediction reports, invited reviews, and topic proposals. In addition, ''Proteins'' includes a section entitled "''Section Notes''", describing novel protein structures. Abstracting and indexing ''Proteins'' 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BLAST
Blast or The Blast may refer to: *Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film), starring Andrew Divoff * ''Blast'' (2000 film), starring Liesel Matthews * ''Blast'' (2004 film), an action comedy film * ''Blast!'' (1972 film) or ''The Final Comedown'', an American drama * ''BLAST!'' (2008 film), a documentary about the BLAST telescope * ''A Blast'', a 2014 film directed by Syllas Tzoumerkas Magazines * ''Blast'' (magazine), a 1914–15 literary magazine of the Vorticist movement * ''Blast'' (U.S. magazine), a 1933–34 American short-story magazine * ''The Blast'' (magazine), a 1916–17 American anarchist periodical Music * Blast (American band), a hardcore punk band * Blast (Russian band), an indie band * ''Blast'' (album), by Holly Johnson, 1989 * ''The Blast'' (album), by Yuvan Shankar Raja, 1999 * "T ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
HHpred / HHsearch
The HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. Sequence searches are a standard tool in modern biology with which the function of unknown proteins can be inferred from the functions of proteins with similar sequences. HHsearch and HHblits are two main programs in the package and the entry point to its search function, the latter being a faster iteration. HHpred is an online server for protein structure prediction that uses homology information from HH-suite. The HH-suite searches for sequences using hidden Markov models (HMMs). The name comes from the fact that it performs HMM-HMM alignments. Among the most popular methods for protein sequence matching, the programs have been cited more than 5000 times total according to Google Scholar. Background Proteins are central players in all of life's processes. Understanding them is central to un ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phyre2
Phyre and Phyre2 (Protein Homology/AnalogY Recognition Engine; pronounced as 'fire') are free web-based services for protein structure prediction. Phyre is among the most popular methods for protein structure prediction having been cited over 1500 times. Like other remote homology recognition techniques (see protein threading), it is able to regularly generate reliable protein models when other widely used methods such as PSI-BLAST cannot. Phyre2 has been designed to ensure a user-friendly interface for users inexpert in protein structure prediction methods. Its development is funded by the Biotechnology and Biological Sciences Research Council. Description The Phyre and Phyre2 servers predict the three-dimensional structure of a protein sequence using the principles and techniques of homology modeling. Because the structure of a protein is more conserved in evolution than its amino acid sequence, a protein sequence of interest (the target) can be modeled with reasonable accuracy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Global Distance Test
The global distance test (GDT), also written as GDT_TS to represent "total score", is a measure of similarity between two protein structures with known amino acid correspondences (e.g. identical amino acid sequences) but different tertiary structures. It is most commonly used to compare the results of protein structure prediction to the experimentally determined structure as measured by X-ray crystallography, protein NMR, or, increasingly, cryoelectron microscopy. The metric was developed by Adam Zemla at Lawrence Livermore National Laboratory and originally implemented in the Local-Global Alignment (LGA) program. It is intended as a more accurate measurement than the common root-mean-square deviation (RMSD) metric - which is sensitive to outlier regions created, for example, by poor modeling of individual loop regions in a structure that is otherwise reasonably accurate. The conventional GDT_TS score is computed over the alpha carbon atoms and is reported as a percentage, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RMSD
The root-mean-square deviation (RMSD) or root-mean-square error (RMSE) is a frequently used measure of the differences between values (sample or population values) predicted by a model or an estimator and the values observed. The RMSD represents the square root of the second sample moment of the differences between predicted values and observed values or the quadratic mean of these differences. These deviations are called '' residuals'' when the calculations are performed over the data sample that was used for estimation and are called ''errors'' (or prediction errors) when computed out-of-sample. The RMSD serves to aggregate the magnitudes of the errors in predictions for various data points into a single measure of predictive power. RMSD is a measure of accuracy, to compare forecasting errors of different models for a particular dataset and not between datasets, as it is scale-dependent. RMSD is always non-negative, and a value of 0 (almost never achieved in practice) would i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Site-directed Mutagenesis
Site-directed mutagenesis is a molecular biology method that is used to make specific and intentional mutating changes to the DNA sequence of a gene and any gene products. Also called site-specific mutagenesis or oligonucleotide-directed mutagenesis, it is used for investigating the structure and biological activity of DNA, RNA, and protein molecules, and for protein engineering. Site-directed mutagenesis is one of the most important laboratory techniques for creating DNA libraries by introducing mutations into DNA sequences. There are numerous methods for achieving site-directed mutagenesis, but with decreasing costs of oligonucleotide synthesis, artificial gene synthesis is now occasionally used as an alternative to site-directed mutagenesis. Since 2013, the development of the CRISPR/Cas9 technology, based on a prokaryotic viral defense system, has also allowed for the editing of the genome, and mutagenesis may be performed ''in vivo'' with relative ease. History Early attempt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Replacement
Molecular replacement (or MR) is a method of solving the phase problem in X-ray crystallography. MR relies upon the existence of a previously solved protein structure which is similar to our unknown structure from which the diffraction data is derived. This could come from a homologous protein, or from the lower-resolution protein NMR structure of the same protein. The first goal of the crystallographer is to obtain an electron density map, density being related with diffracted wave as follows: \rho(x,y,z)=\frac\sum_h\sum_k\sum_l, F_, \exp(2\pi i(hx+ky+lz)+i\Phi(hkl)). With usual detectors the intensity I=F\cdot F^* is being measured, and all the information about phase (\Phi) is lost. Then, in the absence of phases (Φ), we are unable to complete the shown Fourier transform relating the experimental data from X-ray crystallography (in reciprocal space) to real-space electron density, into which the atomic model is built. MR tries to find the model which fits best experimental i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 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] |
