Iterative methodIn computational mathematics, an iterative method is a mathematical procedure that uses an initial value to generate a sequence of improving approximate solutions for a class of problems, in which the n-th approximation is derived from the previous ones. A specific implementation with termination criteria for a given iterative method like gradient descent, hill climbing, Newton's method, or quasi-Newton methods like BFGS, is an algorithm of the iterative method.
Jacobi methodIn numerical linear algebra, the Jacobi method (a.k.a. the Jacobi iteration method) is an iterative algorithm for determining the solutions of a strictly diagonally dominant system of linear equations. Each diagonal element is solved for, and an approximate value is plugged in. The process is then iterated until it converges. This algorithm is a stripped-down version of the Jacobi transformation method of matrix diagonalization. The method is named after Carl Gustav Jacob Jacobi.
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.
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.
Quadratic formIn mathematics, a quadratic form is a polynomial with terms all of degree two ("form" is another name for a homogeneous polynomial). For example, is a quadratic form in the variables x and y. The coefficients usually belong to a fixed field K, such as the real or complex numbers, and one speaks of a quadratic form over K. If , and the quadratic form equals zero only when all variables are simultaneously zero, then it is a definite quadratic form; otherwise it is an isotropic quadratic form.
Cholesky decompositionIn linear algebra, the Cholesky decomposition or Cholesky factorization (pronounced ʃəˈlɛski ) is a decomposition of a Hermitian, positive-definite matrix into the product of a lower triangular matrix and its conjugate transpose, which is useful for efficient numerical solutions, e.g., Monte Carlo simulations. It was discovered by André-Louis Cholesky for real matrices, and posthumously published in 1924. When it is applicable, the Cholesky decomposition is roughly twice as efficient as the LU decomposition for solving systems of linear equations.
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.
Gradient descentIn mathematics, gradient descent (also often called steepest descent) is a iterative optimization algorithm for finding a local minimum of a differentiable function. The idea is to take repeated steps in the opposite direction of the gradient (or approximate gradient) of the function at the current point, because this is the direction of steepest descent. Conversely, stepping in the direction of the gradient will lead to a local maximum of that function; the procedure is then known as gradient ascent.
QR decompositionIn linear algebra, a QR decomposition, also known as a QR factorization or QU factorization, is a decomposition of a matrix A into a product A = QR of an orthonormal matrix Q and an upper triangular matrix R. QR decomposition is often used to solve the linear least squares problem and is the basis for a particular eigenvalue algorithm, the QR algorithm. Any real square matrix A may be decomposed as where Q is an orthogonal matrix (its columns are orthogonal unit vectors meaning ) and R is an upper triangular matrix (also called right triangular matrix).
Orthogonal polynomialsIn mathematics, an orthogonal polynomial sequence is a family of polynomials such that any two different polynomials in the sequence are orthogonal to each other under some inner product. The most widely used orthogonal polynomials are the classical orthogonal polynomials, consisting of the Hermite polynomials, the Laguerre polynomials and the Jacobi polynomials. The Gegenbauer polynomials form the most important class of Jacobi polynomials; they include the Chebyshev polynomials, and the Legendre polynomials as special cases.
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.
LU decompositionIn numerical analysis and linear algebra, lower–upper (LU) decomposition or factorization factors a matrix as the product of a lower triangular matrix and an upper triangular matrix (see matrix decomposition). The product sometimes includes a permutation matrix as well. LU decomposition can be viewed as the matrix form of Gaussian elimination. Computers usually solve square systems of linear equations using LU decomposition, and it is also a key step when inverting a matrix or computing the determinant of a matrix.
Protein primary structureProtein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequencess.
Conjugate gradient methodIn mathematics, the conjugate gradient method is an algorithm for the numerical solution of particular systems of linear equations, namely those whose matrix is positive-definite. The conjugate gradient method is often implemented as an iterative algorithm, applicable to sparse systems that are too large to be handled by a direct implementation or other direct methods such as the Cholesky decomposition. Large sparse systems often arise when numerically solving partial differential equations or optimization problems.
Isotropic quadratic formIn mathematics, a quadratic form over a field F is said to be isotropic if there is a non-zero vector on which the form evaluates to zero. Otherwise the quadratic form is anisotropic. More explicitly, if q is a quadratic form on a vector space V over F, then a non-zero vector v in V is said to be isotropic if q(v) = 0. A quadratic form is isotropic if and only if there exists a non-zero isotropic vector (or null vector) for that quadratic form. Suppose that (V, q) is quadratic space and W is a subspace of V.
Successive over-relaxationIn numerical linear algebra, the method of successive over-relaxation (SOR) is a variant of the Gauss–Seidel method for solving a linear system of equations, resulting in faster convergence. A similar method can be used for any slowly converging iterative process. It was devised simultaneously by David M. Young Jr. and by Stanley P. Frankel in 1950 for the purpose of automatically solving linear systems on digital computers. Over-relaxation methods had been used before the work of Young and Frankel.
Ε-quadratic formIn mathematics, specifically the theory of quadratic forms, an ε-quadratic form is a generalization of quadratic forms to skew-symmetric settings and to *-rings; ε = ±1, accordingly for symmetric or skew-symmetric. They are also called -quadratic forms, particularly in the context of surgery theory. There is the related notion of ε-symmetric forms, which generalizes symmetric forms, skew-symmetric forms (= symplectic forms), Hermitian forms, and skew-Hermitian forms.
Definite quadratic formIn mathematics, a definite quadratic form is a quadratic form over some real vector space V that has the same sign (always positive or always negative) for every non-zero vector of V. According to that sign, the quadratic form is called positive-definite or negative-definite. A semidefinite (or semi-definite) quadratic form is defined in much the same way, except that "always positive" and "always negative" are replaced by "never negative" and "never positive", respectively.
System of linear equationsIn mathematics, a system of linear equations (or linear system) is a collection of one or more linear equations involving the same variables. For example, is a system of three equations in the three variables x, y, z. A solution to a linear system is an assignment of values to the variables such that all the equations are simultaneously satisfied. A solution to the system above is given by the ordered triple since it makes all three equations valid. The word "system" indicates that the equations should be considered collectively, rather than individually.
Linear equationIn mathematics, a linear equation is an equation that may be put in the form where are the variables (or unknowns), and are the coefficients, which are often real numbers. The coefficients may be considered as parameters of the equation, and may be arbitrary expressions, provided they do not contain any of the variables. To yield a meaningful equation, the coefficients are required to not all be zero. Alternatively, a linear equation can be obtained by equating to zero a linear polynomial over some field, from which the coefficients are taken.
