Constraint (mathematics)In mathematics, a constraint is a condition of an optimization problem that the solution must satisfy. There are several types of constraints—primarily equality constraints, inequality constraints, and integer constraints. The set of candidate solutions that satisfy all constraints is called the feasible set. The following is a simple optimization problem: subject to and where denotes the vector (x1, x2). In this example, the first line defines the function to be minimized (called the objective function, loss function, or cost function).
Pseudoconvex functionIn convex analysis and the calculus of variations, both branches of mathematics, a pseudoconvex function is a function that behaves like a convex function with respect to finding its local minima, but need not actually be convex. Informally, a differentiable function is pseudoconvex if it is increasing in any direction where it has a positive directional derivative. The property must hold in all of the function domain, and not only for nearby points.
Docking (molecular)In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction.
Scoring functions for dockingIn the fields of computational chemistry and molecular modelling, scoring functions are mathematical functions used to approximately predict the binding affinity between two molecules after they have been docked. Most commonly one of the molecules is a small organic compound such as a drug and the second is the drug's biological target such as a protein receptor. Scoring functions have also been developed to predict the strength of intermolecular interactions between two proteins or between protein and DNA.
Interior-point methodInterior-point methods (also referred to as barrier methods or IPMs) are a certain class of algorithms that solve linear and nonlinear convex optimization problems. An interior point method was discovered by Soviet mathematician I. I. Dikin in 1967 and reinvented in the U.S. in the mid-1980s. In 1984, Narendra Karmarkar developed a method for linear programming called Karmarkar's algorithm, which runs in provably polynomial time and is also very efficient in practice.
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.
Ant colony optimization algorithmsIn computer science and operations research, the ant colony optimization algorithm (ACO) is a probabilistic technique for solving computational problems which can be reduced to finding good paths through graphs. Artificial ants stand for multi-agent methods inspired by the behavior of real ants. The pheromone-based communication of biological ants is often the predominant paradigm used. Combinations of artificial ants and local search algorithms have become a method of choice for numerous optimization tasks involving some sort of graph, e.
Multi-objective optimizationMulti-objective optimization or Pareto optimization (also known as multi-objective programming, vector optimization, multicriteria optimization, or multiattribute optimization) is an area of multiple-criteria decision making that is concerned with mathematical optimization problems involving more than one objective function to be optimized simultaneously. Multi-objective is a type of vector optimization that has been applied in many fields of science, including engineering, economics and logistics where optimal decisions need to be taken in the presence of trade-offs between two or more conflicting objectives.
Theoretical chemistryTheoretical chemistry is the branch of chemistry which develops theoretical generalizations that are part of the theoretical arsenal of modern chemistry: for example, the concepts of chemical bonding, chemical reaction, valence, the surface of potential energy, molecular orbitals, orbital interactions, and molecule activation. Theoretical chemistry unites principles and concepts common to all branches of chemistry. Within the framework of theoretical chemistry, there is a systematization of chemical laws, principles and rules, their refinement and detailing, the construction of a hierarchy.
Convex functionIn mathematics, a real-valued function is called convex if the line segment between any two distinct points on the graph of the function lies above the graph between the two points. Equivalently, a function is convex if its epigraph (the set of points on or above the graph of the function) is a convex set. A twice-differentiable function of a single variable is convex if and only if its second derivative is nonnegative on its entire domain.
