Convex optimizationConvex optimization is a subfield of mathematical optimization that studies the problem of minimizing convex functions over convex sets (or, equivalently, maximizing concave functions over convex sets). Many classes of convex optimization problems admit polynomial-time algorithms, whereas mathematical optimization is in general NP-hard.
Constrained optimizationIn mathematical optimization, constrained optimization (in some contexts called constraint optimization) is the process of optimizing an objective function with respect to some variables in the presence of constraints on those variables. The objective function is either a cost function or energy function, which is to be minimized, or a reward function or utility function, which is to be maximized.
Mathematical optimizationMathematical optimization (alternatively spelled optimisation) or mathematical programming is the selection of a best element, with regard to some criterion, from some set of available alternatives. It is generally divided into two subfields: discrete optimization and continuous optimization. Optimization problems arise in all quantitative disciplines from computer science and engineering to operations research and economics, and the development of solution methods has been of interest in mathematics for centuries.
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.
Newton's method in optimizationIn calculus, Newton's method (also called Newton–Raphson) is an iterative method for finding the roots of a differentiable function F, which are solutions to the equation F (x) = 0. As such, Newton's method can be applied to the derivative f ′ of a twice-differentiable function f to find the roots of the derivative (solutions to f ′(x) = 0), also known as the critical points of f. These solutions may be minima, maxima, or saddle points; see section "Several variables" in Critical point (mathematics) and also section "Geometric interpretation" in this article.
Structural genomicsStructural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome. This genome-based approach allows for a high-throughput method of structure determination by a combination of experimental and modeling approaches. The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein.
Lagrange multiplierIn mathematical optimization, the method of Lagrange multipliers is a strategy for finding the local maxima and minima of a function subject to equation constraints (i.e., subject to the condition that one or more equations have to be satisfied exactly by the chosen values of the variables). It is named after the mathematician Joseph-Louis Lagrange. The basic idea is to convert a constrained problem into a form such that the derivative test of an unconstrained problem can still be applied.
Multidisciplinary design optimizationMulti-disciplinary design optimization (MDO) is a field of engineering that uses optimization methods to solve design problems incorporating a number of disciplines. It is also known as multidisciplinary system design optimization (MSDO), and Multidisciplinary Design Analysis and Optimization (MDAO). MDO allows designers to incorporate all relevant disciplines simultaneously. The optimum of the simultaneous problem is superior to the design found by optimizing each discipline sequentially, since it can exploit the interactions between the disciplines.
Structural biologyStructural biology is a field that is many centuries old which, as defined by the Journal of Structural Biology, deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes.
Structural alignmentStructural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions.
