Optimization techniques molecular docking

To address the docking problem, techniques for a more global exploration of the en-ag/ landscape are required. A variety of methods is available, frequently used in the context cf other modeling applications and optimization problems as well. Three major classes may be distinguished Monte Carlo techniques, molecular dynamics simulations, and genetic algorithms. Many different vari-fants exist for all of them and frequently, in... 

Virtual screening applications based on superposition or docking usually contain difficult-to-solve optimization problems with a mixed combinatorial and numerical flavor. The combinatorial aspect results from discrete models of conformational flexibility and molecular interactions. The numerical aspect results from describing the relative orientation of two objects, either two superimposed molecules or a ligand with respect to a protein in docking calculations. Problems of this kind are in most cases hard to solve optimally with reasonable compute resources. Sometimes, the combinatorial and the numerical part of such a problem can be separated and independently solved. For example, several virtual screening tools enumerate the conformational space of a molecule in order to address a major combinatorial part of the problem independently (see for example [199]). Alternatively, heuristic search techniques are used to tackle the problem as a whole. Some of them will be covered in this section. 

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