Protein dynamicsProteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis.
Euclidean distanceIn mathematics, the Euclidean distance between two points in Euclidean space is the length of a line segment between the two points. It can be calculated from the Cartesian coordinates of the points using the Pythagorean theorem, therefore occasionally being called the Pythagorean distance. These names come from the ancient Greek mathematicians Euclid and Pythagoras, although Euclid did not represent distances as numbers, and the connection from the Pythagorean theorem to distance calculation was not made until the 18th century.
StructureA structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as biological organisms, minerals and chemicals. Abstract structures include data structures in computer science and musical form. Types of structure include a hierarchy (a cascade of one-to-many relationships), a network featuring many-to-many links, or a lattice featuring connections between components that are neighbors in space.
Sequence motifIn biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an N-glycosylation site motif can be defined as Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro residue. When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical element of the overall structure of the protein.
Intrinsically disordered proteinsIn molecular biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs range from fully unstructured to partially structured and include random coil, molten globule-like aggregates, or flexible linkers in large multi-domain proteins. They are sometimes considered as a separate class of proteins along with globular, fibrous and membrane proteins.
Edit distanceIn computational linguistics and computer science, edit distance is a string metric, i.e. a way of quantifying how dissimilar two strings (e.g., words) are to one another, that is measured by counting the minimum number of operations required to transform one string into the other. Edit distances find applications in natural language processing, where automatic spelling correction can determine candidate corrections for a misspelled word by selecting words from a dictionary that have a low distance to the word in question.
Nth rootIn mathematics, taking the nth root is an operation involving two numbers, the radicand and the index or degree. Taking the nth root is written as , where x is the radicand and n is the index (also sometimes called the degree). This is pronounced as "the nth root of x". The definition then of an nth root of a number x is a number r (the root) which, when raised to the power of the positive integer n, yields x: A root of degree 2 is called a square root (usually written without the n as just ) and a root of degree 3, a cube root (written ).
String metricIn mathematics and computer science, a string metric (also known as a string similarity metric or string distance function) is a metric that measures distance ("inverse similarity") between two text strings for approximate string matching or comparison and in fuzzy string searching. A requirement for a string metric (e.g. in contrast to string matching) is fulfillment of the triangle inequality. For example, the strings "Sam" and "Samuel" can be considered to be close.
Computer simulationComputer simulation is the process of mathematical modelling, performed on a computer, which is designed to predict the behaviour of, or the outcome of, a real-world or physical system. The reliability of some mathematical models can be determined by comparing their results to the real-world outcomes they aim to predict. Computer simulations have become a useful tool for the mathematical modeling of many natural systems in physics (computational physics), astrophysics, climatology, chemistry, biology and manufacturing, as well as human systems in economics, psychology, social science, health care and engineering.
Square (algebra)In mathematics, a square is the result of multiplying a number by itself. The verb "to square" is used to denote this operation. Squaring is the same as raising to the power 2, and is denoted by a superscript 2; for instance, the square of 3 may be written as 32, which is the number 9. In some cases when superscripts are not available, as for instance in programming languages or plain text files, the notations x^2 (caret) or x**2 may be used in place of x2. The adjective which corresponds to squaring is quadratic.
