CORE--Computational Core

CORE--计算核心

• 批准号: 6990378
• 负责人: ARIEH WARSHEL
• 金额: $ 17.44万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-08-16 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6990378
• 关键词: DNA directed DNA polymerase; biomedical facility; computer simulation

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.

Core C将为有效的协作和PPG的理论和实验部分之间的紧密反馈以及对计划项目（PPG）的理论部分提供一些基本支持，为计算支持提供必不可少的计算支持。该核心将对各种蛋白质突变体和DNTP。模板配置进行大规模生成的结构，动力学和热力学数据。它还将提供有效的存储和分析这些数据。与生物化学家和晶体学家密切合作，核心人员将指导有望的蛋白质突变体的选择进行实验分析。通过这种方式，计算核心将提供初始的“筛选”，这将有助于有效进度 PPG的实验部分。因此，我们将Core C的主要功能视为PPG实验努力的扩展，其中模拟代表了实验努力的组成部分。核心还将通过执行一些更“常规”功能来为PPG的计算部分提供重要帮助。总体而言，我们期望核心C提供以下服务：i）筛选氨基酸突变对POL B和POL IV的保真度的影响； ii）过渡状态类似物的自动分析； iii）数据档案，分发和可视化服务； iv）对DNA和DNA聚合酶模拟的力场的细化。