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).
Measure (mathematics)In mathematics, the concept of a measure is a generalization and formalization of geometrical measures (length, area, volume) and other common notions, such as magnitude, mass, and probability of events. These seemingly distinct concepts have many similarities and can often be treated together in a single mathematical context. Measures are foundational in probability theory, integration theory, and can be generalized to assume negative values, as with electrical charge.
Similarity (geometry)In Euclidean geometry, two objects are similar if they have the same shape, or if one has the same shape as the mirror image of the other. More precisely, one can be obtained from the other by uniformly scaling (enlarging or reducing), possibly with additional translation, rotation and reflection. This means that either object can be rescaled, repositioned, and reflected, so as to coincide precisely with the other object. If two objects are similar, each is congruent to the result of a particular uniform scaling of the other.
Levenshtein distanceIn information theory, linguistics, and computer science, the Levenshtein distance is a string metric for measuring the difference between two sequences. Informally, the Levenshtein distance between two words is the minimum number of single-character edits (insertions, deletions or substitutions) required to change one word into the other. It is named after the Soviet mathematician Vladimir Levenshtein, who considered this distance in 1965.
Outer measureIn the mathematical field of measure theory, an outer measure or exterior measure is a function defined on all subsets of a given set with values in the extended real numbers satisfying some additional technical conditions. The theory of outer measures was first introduced by Constantin Carathéodory to provide an abstract basis for the theory of measurable sets and countably additive measures.
DistanceDistance is a numerical or occasionally qualitative measurement of how far apart objects or points are. In physics or everyday usage, distance may refer to a physical length or an estimation based on other criteria (e.g. "two counties over"). Since spatial cognition is a rich source of conceptual metaphors in human thought, the term is also frequently used metaphorically to mean a measurement of the amount of difference between two similar objects (such as statistical distance between probability distributions or edit distance between strings of text) or a degree of separation (as exemplified by distance between people in a social network).
Σ-finite measureIn mathematics, a positive (or signed) measure μ defined on a σ-algebra Σ of subsets of a set X is called a finite measure if μ(X) is a finite real number (rather than ∞), and a set A in Σ is of finite measure if μ(A) < ∞. The measure μ is called σ-finite if X is a countable union of measurable sets each with finite measure. A set in a measure space is said to have σ-finite measure if it is a countable union of measurable sets with finite measure. A measure being σ-finite is a weaker condition than being finite, i.
Similarity measureIn statistics and related fields, a similarity measure or similarity function or similarity metric is a real-valued function that quantifies the similarity between two objects. Although no single definition of a similarity exists, usually such measures are in some sense the inverse of distance metrics: they take on large values for similar objects and either zero or a negative value for very dissimilar objects. Though, in more broad terms, a similarity function may also satisfy metric axioms.
Complete measureIn mathematics, a complete measure (or, more precisely, a complete measure space) is a measure space in which every subset of every null set is measurable (having measure zero). More formally, a measure space (X, Σ, μ) is complete if and only if The need to consider questions of completeness can be illustrated by considering the problem of product spaces. Suppose that we have already constructed Lebesgue measure on the real line: denote this measure space by We now wish to construct some two-dimensional Lebesgue measure on the plane as a product measure.
Jaccard indexThe Jaccard index, also known as the Jaccard similarity coefficient, is a statistic used for gauging the similarity and diversity of sample sets. It was developed by Grove Karl Gilbert in 1884 as his ratio of verification (v) and now is frequently referred to as the Critical Success Index in meteorology. It was later developed independently by Paul Jaccard, originally giving the French name coefficient de communauté, and independently formulated again by T. Tanimoto. Thus, the Tanimoto index or Tanimoto coefficient are also used in some fields.
Borel measureIn mathematics, specifically in measure theory, a Borel measure on a topological space is a measure that is defined on all open sets (and thus on all Borel sets). Some authors require additional restrictions on the measure, as described below. Let be a locally compact Hausdorff space, and let be the smallest σ-algebra that contains the open sets of ; this is known as the σ-algebra of Borel sets. A Borel measure is any measure defined on the σ-algebra of Borel sets.
Vector measureIn mathematics, a vector measure is a function defined on a family of sets and taking vector values satisfying certain properties. It is a generalization of the concept of finite measure, which takes nonnegative real values only.
Protein designProtein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function. Proteins can be designed from scratch (de novo design) or by making calculated variants of a known protein structure and its sequence (termed protein redesign). Rational protein design approaches make protein-sequence predictions that will fold to specific structures.
Biomolecular structureBiomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels: primary, secondary, tertiary, and quaternary.
Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
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.
Square numberIn mathematics, a square number or perfect square is an integer that is the square of an integer; in other words, it is the product of some integer with itself. For example, 9 is a square number, since it equals 32 and can be written as 3 × 3. The usual notation for the square of a number n is not the product n × n, but the equivalent exponentiation n2, usually pronounced as "n squared". The name square number comes from the name of the shape. The unit of area is defined as the area of a unit square (1 × 1).
Homology modelingHomology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence.
Difference of two squaresIn mathematics, the difference of two squares is a squared (multiplied by itself) number subtracted from another squared number. Every difference of squares may be factored according to the identity in elementary algebra. The proof of the factorization identity is straightforward. Starting from the left-hand side, apply the distributive law to get By the commutative law, the middle two terms cancel: leaving The resulting identity is one of the most commonly used in mathematics.
Structural bioinformaticsStructural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models.
