My most recent studies involve the development, parameterization, and testing of knowledge-based atom level interaction potentials. These potentials of mean force (KBpmf) were tested in conjunction with the molecular mechanical potential (MMP) energy function found in the program AMBER. The KBpmf serves as an implicit water solvation potential in diagnostic tests including inverse folding and inverse refinement of single domain protein structures. Other recent studies have involved Molecular Dynamics calculations. These have included an investigation into the details of structure and dynamic motional properties of octanol, including dielectric behavior, molecular dynamics and free energy perturbation studies to determine the structural and energetic effects of partitioning small molecules into nonpolar solvents, particularly n-octanol. The UCSF Computer Graphics Laboratory provides an essential graphic and communications network link between the UCSF Pharmaceutical Chemistry Department and offsite investigators like myself. The CGL facilitates ongoing collaborations between researchers physically located at UCSF with those like myself at other research institutions by permitting visual assessment of shared online structural data, such as the orientations of computer simulated molecules, prediction of protein secondary structure, for monitoring solute/solvent and protein structures time-trajectories, and for appraisal of the accuracy of the configurations generated. The CGL technology also serves an essential role in helping me prepare graphics for scientific presentations and publications.
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