Protein domainIn 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.
Protein structure predictionProtein 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).
Protein–protein interactionProtein–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.
Protein structureProtein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.
GeneIn biology, the word gene (from γένος, génos; meaning generation or birth or gender) can have several different meanings. The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and noncoding genes. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function.
Gene structureGene structure is the organisation of specialised sequence elements within a gene. Genes contain most of the information necessary for living cells to survive and reproduce. In most organisms, genes are made of DNA, where the particular DNA sequence determines the function of the gene. A gene is transcribed (copied) from DNA into RNA, which can either be non-coding (ncRNA) with a direct function, or an intermediate messenger (mRNA) that is then translated into protein.
Gamma distributionIn probability theory and statistics, the gamma distribution is a two-parameter family of continuous probability distributions. The exponential distribution, Erlang distribution, and chi-squared distribution are special cases of the gamma distribution. There are two equivalent parameterizations in common use: With a shape parameter and a scale parameter . With a shape parameter and an inverse scale parameter , called a rate parameter. In each of these forms, both parameters are positive real numbers.
ProteinProteins 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.
Probability distributionIn probability theory and statistics, a probability distribution is the mathematical function that gives the probabilities of occurrence of different possible outcomes for an experiment. It is a mathematical description of a random phenomenon in terms of its sample space and the probabilities of events (subsets of the sample space). For instance, if X is used to denote the outcome of a coin toss ("the experiment"), then the probability distribution of X would take the value 0.5 (1 in 2 or 1/2) for X = heads, and 0.
Chi-squared distributionIn probability theory and statistics, the chi-squared distribution (also chi-square or -distribution) with degrees of freedom is the distribution of a sum of the squares of independent standard normal random variables. The chi-squared distribution is a special case of the gamma distribution and is one of the most widely used probability distributions in inferential statistics, notably in hypothesis testing and in construction of confidence intervals.
RNA splicingRNA splicing is a process in molecular biology where a newly-made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). It works by removing all the introns (non-coding regions of RNA) and splicing back together exons (coding regions). For nuclear-encoded genes, splicing occurs in the nucleus either during or immediately after transcription. For those eukaryotic genes that contain introns, splicing is usually needed to create an mRNA molecule that can be translated into protein.
Protein–protein interaction predictionProtein–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.
Protein function predictionProtein 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.
Gene expressionGene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, and ultimately affect a phenotype. These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA.
Maximum entropy probability distributionIn statistics and information theory, a maximum entropy probability distribution has entropy that is at least as great as that of all other members of a specified class of probability distributions. According to the principle of maximum entropy, if nothing is known about a distribution except that it belongs to a certain class (usually defined in terms of specified properties or measures), then the distribution with the largest entropy should be chosen as the least-informative default.
Instant-runoff votingInstant-runoff voting (IRV) is an electoral system that uses ranked voting. Its purpose is to elect the majority choice in single-member districts in which there are more than two candidates and thus help ensure majority rule. It is a single-winner version of single transferable voting. Formerly the term "instant-runoff voting" was used for what many people now call contingent voting or supplementary vote.
Domain nameIn the Internet, a domain name is a string that identifies a realm of administrative autonomy, authority or control. Domain names are often used to identify services provided through the Internet, such as websites, email services and more. As of 2017, 330.6 million domain names had been registered. Domain names are used in various networking contexts and for application-specific naming and addressing purposes. In general, a domain name identifies a network domain or an Internet Protocol (IP) resource, such as a personal computer used to access the Internet, or a server computer.
Indecomposable distributionIn probability theory, an indecomposable distribution is a probability distribution that cannot be represented as the distribution of the sum of two or more non-constant independent random variables: Z ≠ X + Y. If it can be so expressed, it is decomposable: Z = X + Y. If, further, it can be expressed as the distribution of the sum of two or more independent identically distributed random variables, then it is divisible: Z = X1 + X2. The simplest examples are Bernoulli-distributeds: if then the probability distribution of X is indecomposable.
Pearson distributionThe Pearson distribution is a family of continuous probability distributions. It was first published by Karl Pearson in 1895 and subsequently extended by him in 1901 and 1916 in a series of articles on biostatistics. The Pearson system was originally devised in an effort to model visibly skewed observations. It was well known at the time how to adjust a theoretical model to fit the first two cumulants or moments of observed data: Any probability distribution can be extended straightforwardly to form a location-scale family.
Protein fold classIn molecular biology, protein fold classes are broad categories of protein tertiary structure topology. They describe groups of proteins that share similar amino acid and secondary structure proportions. Each class contains multiple, independent protein superfamilies (i.e. are not necessarily evolutionarily related to one another). Four large classes of protein that are generally agreed upon by the two main structure classification databases (SCOP and CATH).
