Core C will provide the computational support essential for an effective collaboration and a tight feedback between the theoretical and experimental parts of the PPG as well as some basic support for the theoretical part of the program project (PPG). This core will carry out a large-scale generation of structural, kinetic and thermodynamic data for various protein mutants and dNTP.template configurations. It will also provide an efficient storage and analysis of these data. Closely collaborating with biochemists and crystallographers, the core personnel will guide the selection of promising protein mutants for experimental analysis. In this way, the computational core will provide an initial """"""""screening"""""""" which will help the effective progress in the experimental part of the PPG. Thus, we view the main function of core C as an extension of the experimental effort of the PPG, where the simulations represent an integral part of the experimental effort. The core will also provide important help to the computational part of the PPG by performing some of the more """"""""routine"""""""" functions. Overall we expect Core C to provide the following services: i) Screening the effects of aminoacid mutations on the fidelity of pol b and pol IV; ii) Automated analysis of transition state analogues; iii) Data archival, distribution, and visualization services; iv) Refinement of force fields for simulations of DNA and DNA polymerases.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Program--Cooperative Agreements (U19)
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Subcommittee G - Education (NCI)
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University of Southern California
Los Angeles
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