Short linear motifIn molecular biology short linear motifs (SLiMs), linear motifs or minimotifs are short stretches of protein sequence that mediate protein–protein interaction. The first definition was given by Tim Hunt: "The sequences of many proteins contain short, conserved motifs that are involved in recognition and targeting activities, often separate from other functional properties of the molecule in which they occur. These motifs are linear, in the sense that three-dimensional organization is not required to bring distant segments of the molecule together to make the recognizable unit.
InteractomeIn 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.
Stochastic block modelThe stochastic block model is a generative model for random graphs. This model tends to produce graphs containing communities, subsets of nodes characterized by being connected with one another with particular edge densities. For example, edges may be more common within communities than between communities. Its mathematical formulation has been firstly introduced in 1983 in the field of social network by Paul W. Holland et al.
Automatic differentiationIn mathematics and computer algebra, automatic differentiation (auto-differentiation, autodiff, or AD), also called algorithmic differentiation, computational differentiation, is a set of techniques to evaluate the partial derivative of a function specified by a computer program. Automatic differentiation exploits the fact that every computer calculation, no matter how complicated, executes a sequence of elementary arithmetic operations (addition, subtraction, multiplication, division, etc.
UnderstandingUnderstanding is a cognitive process related to an abstract or physical object, such as a person, situation, or message whereby one is able to use concepts to model that object. Understanding is a relation between the knower and an object of understanding. Understanding implies abilities and dispositions with respect to an object of knowledge that are sufficient to support intelligent behavior. Understanding is often, though not always, related to learning concepts, and sometimes also the theory or theories associated with those concepts.
Canonical formIn mathematics and computer science, a canonical, normal, or standard form of a mathematical object is a standard way of presenting that object as a mathematical expression. Often, it is one which provides the simplest representation of an object and allows it to be identified in a unique way. The distinction between "canonical" and "normal" forms varies from subfield to subfield. In most fields, a canonical form specifies a unique representation for every object, while a normal form simply specifies its form, without the requirement of uniqueness.
InterProInterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them. The contents of InterPro consist of diagnostic signatures and the proteins that they significantly match. The signatures consist of models (simple types, such as regular expressions or more complex ones, such as Hidden Markov models) which describe protein families, domains or sites.
ClustalClustal is a series of widely used computer programs used in bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below. The analysis of each tool and its algorithm is also detailed in their respective categories. Available operating systems listed in the sidebar are a combination of the software availability and may not be supported for every current version of the Clustal tools.
BioprospectingBioprospecting (also known as biodiversity prospecting) is the exploration of natural sources for small molecules, macromolecules and biochemical and genetic information that could be developed into commercially valuable products for the agricultural, aquaculture, bioremediation, cosmetics, nanotechnology, or pharmaceutical industries. In the pharmaceutical industry, for example, almost one third of all small-molecule drugs approved by the U.S.
