CORE--Computational Core

核心C将为PPG的理论和实验部分之间的有效协作和紧密反馈提供必要的计算支持，并为计划项目(PPG)的理论部分提供一些基本支持。该核心将对各种蛋白质突变体和dNTP模板配置进行大规模的结构、动力学和热力学数据的生成。它还将提供对这些数据的有效存储和分析。核心人员将与生物化学家和结晶学家密切合作，指导选择有希望的蛋白质突变体进行实验分析。通过这种方式，计算核心将提供初步的“筛选”，这将有助于在 PPG的实验部分。因此，我们将核心C的主要功能视为PPG实验工作的延伸，其中模拟代表实验工作的组成部分。该核心还将通过执行一些更“例行公事”的功能，为PPG的计算部分提供重要帮助。总体而言，我们预计Core C将提供以下服务：i)筛选氨基酸突变对Polb和PolIV保真度的影响；ii)过渡态类似物的自动分析；iii)数据存档、分配和可视化服务；iv)改进用于模拟DNA和DNA聚合酶的力场。

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.