My most recent studies involve the development, parameterization, and testing of atom level molecular mechanical interaction potentials. The interaction potential is being designed specifically for use in de novo predictions of the location of explicit water molecules in enzyme/inhibitor complexes. It is being tested on a database of """"""""knowns"""""""", complexes compiled from the Brookhaven Protein Data Base. A search of the UCSF Computer Graphics Lab's well organized and indexed version of the PDB (o find high resolution enzyme/inhibitor complexes) was extremely helpful in getting this research off to a strong start. Now that the project is well towards completion, I have just recently used the CGL database to help me determine which enzyme/ligand complex structures will serve as """"""""unknowns"""""""" for testing the water placement algorithm. Our recent work demonstrates the influence of bound water molecules at the active site complex of protein FKBP and the competitively bound solvent DMSO. Other recent studies include the development and testing of a water molecule placement algorithm. 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 corporate 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 collaborating me prepare graphics for scientific presentations and publications.
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