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Protein–protein Interaction Prediction
Protein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining insights into various biochemical processes. ''Experimentally'', physical interactions between pairs of proteins can be inferred from a variety of techniques, including yeast two-hybrid screening, two-hybrid systems, Protein-fragment complementation assay, protein-fragment complementation assays (PCA), affinity purification/mass spectrometry, protein microarrays, fluorescence resonance energy transfer (FRET), and Microscale Thermophoresis (MST). Efforts to experimentally determine the interactome of numerous species are ongoing. Experimentally determined interactions usually provide the basis for ''computational methods' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SH3 Domain
The SRC Homology 3 Domain (or SH3 domain) is a small protein domain of about 60 amino acid residues. Initially, SH3 was described as a conserved sequence in the viral adaptor protein v-Crk. This domain is also present in the molecules of phospholipase and several cytoplasmic tyrosine kinases such as Abl and Src. It has also been identified in several other protein families such as: PI3 Kinase, Ras GTPase-activating protein, CDC24 and cdc25. SH3 domains are found in proteins of signaling pathways regulating the cytoskeleton, the Ras protein, and the Src kinase and many others. The SH3 proteins interact with adaptor proteins and tyrosine kinases. Interacting with tyrosine kinases, SH3 proteins usually bind far away from the active site. Approximately 300 SH3 domains are found in proteins encoded in the human genome. In addition to that, the SH3 domain was responsible for controlling protein-protein interactions in the signal transduction pathways and regulating the ... [...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 Protein secondary structure, secondary and Protein tertiary structure, tertiary structure from Protein primary structure, 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 addresses Levinthal's paradox. Accurate structure prediction has important applications in medicine (for example, in drug design) and biotechnology (for example, in novel enzyme design). Starting in 1994, the performance of current methods is assessed biannually in the ''Critical Assessment of Structure Prediction'' (CASP) experiment. A continuous evaluation of protein structure prediction web servers is performed by the community project ''Continuous Automated Model EvaluatiOn'' (CAMEO3D). Protein structure a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Function Prediction
Protein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. These predictions are often driven by data-intensive computational procedures. Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of publications, phylogenetic profiles, phenotypic profiles, and protein-protein interaction. Protein function is a broad term: the roles of proteins range from catalysis of biochemical reactions to transport to signal transduction, and a single protein may play a role in multiple processes or cellular pathways. Generally, function can be thought of as, "anything that happens to or through a protein". The Gene Ontology Consortium provides a useful classification of functions, based on a dictionary of well-defined terms divided into three main ca ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein–protein Interaction
Protein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context. Proteins rarely act alone as their functions tend to be regulated. Many molecular processes within a cell are carried out by molecular machines that are built from numerous protein components organized by their PPIs. These physiological interactions make up the so-called Interactome, interactomics of the organism, while aberrant PPIs are the basis of multiple aggregation-related diseases, such as Creutzfeldt–Jakob disease, Creutzfeldt–Jakob and Alzheimer's diseases. PPIs have been studied with Methods to investigate protein–protein interactions, many methods and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Interactome
In molecular biology, an interactome is the whole set of molecular interactions in a particular cell. The term specifically refers to physical interactions among molecules (such as those among proteins, also known as protein–protein interactions, PPIs; or between small molecules and proteins) but can also describe sets of indirect interactions among genes ( genetic interactions). The word "interactome" was originally coined in 1999 by a group of French scientists headed by Bernard Jacq. Mathematically, interactomes are generally displayed as graphs. While interactomes may be described as biological networks, they should not be confused with other networks such as neural networks or food webs. Molecular interaction networks Molecular interactions can occur between molecules belonging to different biochemical families (proteins, nucleic acids, lipids, carbohydrates, etc.) and also within a given family. Whenever such molecules are connected by physical interactions, they form m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein-protein Docking
Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Protein–protein complexes are the most commonly attempted targets of such modelling, followed by protein–nucleic acid complexes. The ultimate goal of docking is the prediction of the three-dimensional structure of the macromolecular complex of interest as it would occur in a living organism. Docking itself only produces plausible candidate structures. These candidates must be ranked using methods such as scoring functions to identify structures that are most likely to occur in nature. The term "docking" originated in the late 1970s, with a more restricted meaning; then, "docking" meant refining a model of a complex structure by optimizing the separation between the interactors but keeping their relative orientations fixed. Later, the relative orientations of the interacting partners in the modelling was allowed to var ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bayesian Method
Bayesian inference ( or ) is a method of statistical inference in which Bayes' theorem is used to calculate a probability of a hypothesis, given prior evidence, and update it as more information becomes available. Fundamentally, Bayesian inference uses a prior distribution to estimate posterior probabilities. Bayesian inference is an important technique in statistics, and especially in mathematical statistics. Bayesian updating is particularly important in the dynamic analysis of a sequence of data. Bayesian inference has found application in a wide range of activities, including science, engineering, philosophy, medicine, sport, and law. In the philosophy of decision theory, Bayesian inference is closely related to subjective probability, often called "Bayesian probability". Introduction to Bayes' rule Formal explanation Bayesian inference derives the posterior probability as a consequence of two antecedents: a prior probability and a "likelihood function" derived from ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Van Der Waals Radius
The van der Waals radius, ''r'', of an atom is the radius of an imaginary hard sphere representing the distance of closest approach for another atom. It is named after Johannes Diderik van der Waals, winner of the 1910 Nobel Prize in Physics, as he was the first to recognise that atoms were not simply points and to demonstrate the physical consequences of their size through the van der Waals equation of state. van der Waals volume The van der Waals volume, ''V'', also called the atomic volume or molecular volume, is the atomic property most directly related to the van der Waals radius. It is the volume "occupied" by an individual atom (or molecule). The van der Waals volume may be calculated if the van der Waals radii (and, for molecules, the inter-atomic distances, and angles) are known. For a single atom, it is the volume of a sphere whose radius is the van der Waals radius of the atom:V_ = \pi r_^3. For a molecule, it is the volume enclosed by the van der Waals surf ... [...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] |
Interolog
An interolog is a conserved interaction between a pair of proteins which have interacting Homology (biology), homologs in another organism. The term was introduced in a 2000 paper by Walhout et al. Example Suppose that A and B are two different interacting human proteins, and A' and B' are two different interacting dog proteins. Then the interaction between A and B is an interolog of the interaction between A' and B' if the following conditions all hold: *A is a homolog of A'. (Protein homologs have similar amino acid sequences and derive from a common ancestral sequence). *B is a homolog of B'. *A and B interact. *A' and B' interact. Thus, interologs are homologous pairs of protein interactions across different organisms. See also *Homology (biology) *Systems biology *Bioinformatics References * * * External links Interactome.org: Interactome portal site. * : Interactomics portal site. Cross-species interaction prediction site. Protein complexes Bioinformatics ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tryptophan Synthase
Tryptophan synthase or tryptophan synthetase is an enzyme () that catalyzes the final two steps in the biosynthesis of tryptophan. It is commonly found in Eubacteria, Archaebacteria, Protista, Fungi, and Plantae. However, it is absent from Animalia. It is typically found as an α2β2 tetramer. The α subunits catalyze the reversible formation of indole and glyceraldehyde-3-phosphate (G3P) from indole-3-glycerol phosphate (IGP). The β subunits catalyze the irreversible condensation of indole and serine to form tryptophan in a pyridoxal phosphate (PLP) dependent reaction. Each α active site is connected to a β active site by a 25 Ångstrom long hydrophobic channel contained within the enzyme. This facilitates the diffusion of indole formed at α active sites directly to β active sites in a process known as substrate channeling. The active sites of tryptophan synthase are allosterically coupled. Enzyme structure Subunits Tryptophan synthase typically exists as an α-ββ-α ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
