The long term goal of this project is the development of a new method for determining the lowest energy structure of molecules. This method could be applied to the determination of, for example, the three dimensional structure of proteins from the primary amino acid sequence. The end result of this particular study will be a demonstration of the use of the genetic optimization technique with molecular mechanics to find the energy minimum structure of a simple dipeptide whose conformational energy map is well known. Molecular structure determination involves a search of a large conformational space containing many stable structures but only a relatively small number of important low energy structures. The Genetic optimization technique has been successfully applied to difficult search problems with characteristics similar to the molecular domain. It is based upon the mechanics of natural genetics, in which the desirable features of a set of structures are combined through randomized information exchange to produce new structures with improved characteristics. Applied to the molecular structure determination problem, the features of a set of """"""""parent"""""""" molecular configurations that lead to low energy structures are combined through specific genetic operations to produce """"""""offspring"""""""" structures that could result in even lower energy structures. The prototype implementation resulting from this study will be used to further develop this technique to compute the lowest energy structure of macromolecules.
