STRUCTURE BASED PREDICTION OF CONFORMATIONAL & BINDING FREE ENERGIES

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The goal of the research described in this proposal is the calculation to conformational free energies and binding free energies relevant to the structure and function of biological macromolecules. The specific problems of interest include the indentification of stable protein folds, the binding of drugs to the HIV protease and to the minor groove of DNA, and the binding of peptides and proteins to the surface of membranes. The overall strategy is to use molecular dynamics calculations to generate stable conformations, to evaluate their gas phase energies using molecular mechanics force fields, and to evaluate solvation free energies using continuum solvent models. The sum of the gas phase and solvation free energies yield conformational and binding free energies. The request is for sufficient computer time to carry out production runs on the specific problems of interest.