MOLECULAR DYNAMICS SIMULATIONS OF NUCLEIC ACIDS: STRUCTURE, MOTIONS, SOLVATION

核酸的分子动力学模拟：结构、运动、溶剂化

• 批准号: 7601381
• 负责人: DAVID L BEVERIDGE
• 金额: $ 0.03万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7601381
• 关键词: Complex; Computer Retrieval of Information on Scientific Projects Database; Computer Simulation; DNA; DNA Structure; Equilibrium; Free Energy; Funding; Grant; Institution; Joints; Motion; Nucleic Acids; Proteins; RNA; Research; Research Personnel; Resources; Source; System; United States National Institutes of Health; Validation; base; models and simulation; molecular dynamics; molecular modeling; nucleic acid structure

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our proposed research involves studies of the dynamical structures of DNA and RNA nucleic acids and their complexes with proteins based on molecular modeling via computer simulation and related theoretical approaches. The overall reliability of molecular modeling and simulation on DNA and RNA systems depends critically on the demonstrable accuracy of the calculated results. Thus, one of the focal points of this research is critical validation and assessment of one of most detailed form of computational modeling, all-atom molecular dynamics (MD) simulation. An additional emphasis in the proposed project period will be the articulation of free energy calculations with MD in order to approach more directly diverse questions about stability and conformational equilibria of nucleic acids structures and their complexes.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目和 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 我们提出的研究涉及基于计算机模拟和相关理论方法的分子建模，研究 DNA 和 RNA 核酸及其与蛋白质的复合物的动态结构。 DNA 和 RNA 系统分子建模和模拟的整体可靠性关键取决于计算结果的可证明准确性。因此，这项研究的重点之一是对最详细的计算建模形式之一——全原子分子动力学（MD）模拟的关键验证和评估。拟议项目期间的另一个重点是通过分子动力学进行自由能计算，以便更直接地解决有关核酸结构及其复合物的稳定性和构象平衡的各种问题。