Continuous Optimization Methods for Structure Alignments

Structural Alignment is an important tool for fold identification of proteins, structural screening on ligand databases, pharmacophore identification and other applications. In the general case, the optimization problem of superimposing two structures is nonsmooth and nonconvex, so that most popular methods are heuristic and do not employ derivative information. Usually, these methods do not admit … Read more

Low Order-Value Optimization and Applications

Given r real functions F1 (x), . . . , Fr (x) and an integer p between 1 and r, the Low Order- Value Optimization problem (LOVO) consists of minimizing the sum of the functions that take the p smaller values. If (y1 , . . . , yr ) is a vector of data … Read more

Nonlinear-Programming Reformulation of the Order-Value Optimization problem

Order-value optimization (OVO) is a generalization of the minimax problem motivated by decision-making problems under uncertainty and by robust estimation. New optimality conditions for this nonsmooth optimization problem are derived. An equivalent mathematical programming problem with equilibrium constraints is deduced. The relation between OVO and this nonlinear-programming reformulation is studied. Particular attention is given to … Read more