CORE--Computational Core

核心C将提供有效合作所必需的计算支持和PPG的理论和实验部分之间的紧密反馈，以及对程序项目（PPG）的理论部分的一些基本支持。该核心将进行各种蛋白质突变体和dNTP模板配置的结构，动力学和热力学数据的大规模生成。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晶体学家密切合作，指导选择有前途的蛋白质突变体进行实验分析。通过这种方式，计算核心将提供一个初始的“筛选”，这将有助于有效的进展， PPG的实验部分。因此，我们认为核心C的主要功能是PPG实验工作的扩展，其中模拟代表实验工作的一个组成部分。核心还将通过执行一些更“常规”的功能，为PPG的计算部分提供重要帮助。总的来说，我们希望核心C提供以下服务：i）筛选氨基酸突变对pol B和pol IV保真度的影响; ii）过渡态类似物的自动分析; iii）数据存档，分发和可视化服务; iv）优化用于DNA和DNA聚合酶模拟的力场。

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.