Abstract
Conformational search or global energy optimization procedures constitute the core for many applications of molecular modeling such as protein design and engineering, modeling by homology, structure determination from NMR data, and structure analysis and refinement. Factors complicating global optimization include the high dimensionality of conformational space, accompanied by strong anisotropy of the energy hypersurface and a large number of local minima as well as inaccuracies in calculating energy. Several global search protocols, based on Monte Carlo procedures, are compared and optimized. Performance criteria are reformulated and corresponding techniques for accumulating and clustering the optimal conformations found during a search are developed and applied to Met-enkephalin.
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