Protein secondary structureProtein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone.
Linear combinationIn mathematics, a linear combination is an expression constructed from a set of terms by multiplying each term by a constant and adding the results (e.g. a linear combination of x and y would be any expression of the form ax + by, where a and b are constants). The concept of linear combinations is central to linear algebra and related fields of mathematics. Most of this article deals with linear combinations in the context of a vector space over a field, with some generalizations given at the end of the article.
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.
Linear spanIn mathematics, the linear span (also called the linear hull or just span) of a set S of vectors (from a vector space), denoted span(S), is defined as the set of all linear combinations of the vectors in S. For example, two linearly independent vectors span a plane. The linear span can be characterized either as the intersection of all linear subspaces that contain S, or as the smallest subspace containing S. The linear span of a set of vectors is therefore a vector space itself. Spans can be generalized to matroids and modules.
Affine combinationIn mathematics, an affine combination of x1, ..., xn is a linear combination such that Here, x1, ..., xn can be elements (vectors) of a vector space over a field K, and the coefficients are elements of K. The elements x1, ..., xn can also be points of a Euclidean space, and, more generally, of an affine space over a field K. In this case the are elements of K (or for a Euclidean space), and the affine combination is also a point. See for the definition in this case.
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).
Linear independenceIn the theory of vector spaces, a set of vectors is said to be if there exists no nontrivial linear combination of the vectors that equals the zero vector. If such a linear combination exists, then the vectors are said to be . These concepts are central to the definition of dimension. A vector space can be of finite dimension or infinite dimension depending on the maximum number of linearly independent vectors. The definition of linear dependence and the ability to determine whether a subset of vectors in a vector space is linearly dependent are central to determining the dimension of a vector space.
Conical combinationGiven a finite number of vectors in a real vector space, a conical combination, conical sum, or weighted sum of these vectors is a vector of the form where are non-negative real numbers. The name derives from the fact that a conical sum of vectors defines a cone (possibly in a lower-dimensional subspace). The set of all conical combinations for a given set S is called the conical hull of S and denoted cone(S) or coni(S). That is, By taking k = 0, it follows the zero vector (origin) belongs to all conical hulls (since the summation becomes an empty sum).
Protein tertiary structureProtein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.
Convolutional neural networkConvolutional neural network (CNN) is a regularized type of feed-forward neural network that learns feature engineering by itself via filters (or kernel) optimization. Vanishing gradients and exploding gradients, seen during backpropagation in earlier neural networks, are prevented by using regularized weights over fewer connections. For example, for each neuron in the fully-connected layer 10,000 weights would be required for processing an image sized 100 × 100 pixels.
Euclidean spaceEuclidean space is the fundamental space of geometry, intended to represent physical space. Originally, that is, in Euclid's Elements, it was the three-dimensional space of Euclidean geometry, but in modern mathematics there are Euclidean spaces of any positive integer dimension n, which are called Euclidean n-spaces when one wants to specify their dimension. For n equal to one or two, they are commonly called respectively Euclidean lines and Euclidean planes.
Protein quaternary structureProtein quaternary structure is the fourth (and highest) classification level of protein structure. Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains (also referred to as subunits). Protein quaternary structure describes the number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits.
Linear subspaceIn mathematics, and more specifically in linear algebra, a linear subspace or vector subspace is a vector space that is a subset of some larger vector space. A linear subspace is usually simply called a subspace when the context serves to distinguish it from other types of subspaces. If V is a vector space over a field K and if W is a subset of V, then W is a linear subspace of V if under the operations of V, W is a vector space over K.
Three-dimensional spaceIn geometry, a three-dimensional space (3D space, 3-space or, rarely, tri-dimensional space) is a mathematical space in which three values (coordinates) are required to determine the position of a point. Most commonly, it is the three-dimensional Euclidean space, the Euclidean n-space of dimension n=3 that models physical space. More general three-dimensional spaces are called 3-manifolds. Technically, a tuple of n numbers can be understood as the Cartesian coordinates of a location in a n-dimensional Euclidean space.
Euclidean planeIn mathematics, a Euclidean plane is a Euclidean space of dimension two, denoted E2. It is a geometric space in which two real numbers are required to determine the position of each point. It is an affine space, which includes in particular the concept of parallel lines. It has also metrical properties induced by a distance, which allows to define circles, and angle measurement. A Euclidean plane with a chosen Cartesian coordinate system is called a Cartesian plane.
Pseudo-Euclidean spaceIn mathematics and theoretical physics, a pseudo-Euclidean space is a finite-dimensional real n-space together with a non-degenerate quadratic form q. Such a quadratic form can, given a suitable choice of basis (e1, ..., en), be applied to a vector x = x1e1 + ⋯ + xnen, giving which is called the scalar square of the vector x. For Euclidean spaces, k = n, implying that the quadratic form is positive-definite. When 0 < k < n, q is an isotropic quadratic form, otherwise it is anisotropic.
Euclidean groupIn mathematics, a Euclidean group is the group of (Euclidean) isometries of a Euclidean space ; that is, the transformations of that space that preserve the Euclidean distance between any two points (also called Euclidean transformations). The group depends only on the dimension n of the space, and is commonly denoted E(n) or ISO(n). The Euclidean group E(n) comprises all translations, rotations, and reflections of ; and arbitrary finite combinations of them.
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).
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.
Euclidean geometryEuclidean geometry is a mathematical system attributed to ancient Greek mathematician Euclid, which he described in his textbook on geometry, Elements. Euclid's approach consists in assuming a small set of intuitively appealing axioms (postulates) and deducing many other propositions (theorems) from these. Although many of Euclid's results had been stated earlier, Euclid was the first to organize these propositions into a logical system in which each result is proved from axioms and previously proved theorems.
