CORE--Computational Core

CORE--计算核心

基本信息

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
项目类别：
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

项目摘要

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 PPG 的理论部分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，并为程序项目 (PPG) 的理论部分提供一些基本支持。该核心将为各种蛋白质突变体和 dNTP.template 配置大规模生成结构、动力学和热力学数据。它还将为这些数据提供有效的存储和分析。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，计算核心将提供初步的“筛选”，这将有助于问题的有效进展。 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，其中模拟代表了实验工作的一个组成部分。该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。总体而言，我们期望Core 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) 数据归档、分发和可视化服务； iv) 精细化模拟 DNA 和 DNA 聚合酶的力场。