METHODS AND APPLICATIONS OF HYBRID QM/MM SIMULATIONS TO BIOMOLECULAR SYSTEMS, S

生物分子系统混合 QM/MM 模拟的方法和应用

• 批准号: 7956290
• 负责人: TROY WYMORE
• 金额: $ 0.08万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956290
• 关键词: Active Sites; Biochemical Reaction; Biomedical Research; Biophysics; Case-Control Studies; Computer Retrieval of Information on Scientific Projects Database; Computers; Educational workshop; Enzymes; Faculty; Free Energy; Funding; Gases; Grant; High Performance Computing; Hybrids; Institution; Libraries; Mechanics; Methods; Modeling; Molecular; Organic Chemistry; Participant; Performance; Phase; Postdoctoral Fellow; Potential Energy; Reaction; Research; Research Personnel; Resources; Solvents; Source; System; Techniques; United States National Institutes of Health; Water; Work; computational chemistry; density; design; experience; graduate student; molecular mechanics; molecular orbital; quantum; simulation; theories

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. The workshop will explore computational approaches for the simulation of enzymatic reactions. The course will present the relevant theoretical background including ab initio and semiempirical molecular orbital methods, density functional theory, molecular mechanics force fields, hybrid Quantum Mechanical/Molecular Mechanical potential energy functions, and simulation techniques on high performance computers. Case studies based on determining the free energy profile for a reaction in the gas phase, in water (using both implicit and explicit solvent) and in an enzyme active site will be presented using primarily the DYNAMO library. Experience with DYNAMO is helpful but not a prerequisite for attendance. The workshop is designed for graduate students, post-doctoral researchers and faculty in computational biophysics and physical organic chemistry who have some experience with computational chemistry methods and seek to enhance their capabilities to include the modeling of enzymatic reactions. Participants are encouraged to discuss and work on biomolecular systems from their own research during the workshop.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 研讨会将探讨酶反应模拟的计算方法。本课程将介绍相关的理论背景，包括从头算和半经验分子轨道方法，密度泛函理论，分子力学力场，混合量子力学/分子力学势能函数，以及高性能计算机上的模拟技术。案例研究的基础上确定的自由能分布在气相中的反应，在水中（使用隐式和显式溶剂），并在酶的活性位点将主要使用的CNOMO库。有参加过国际劳工组织的经验是有帮助的，但不是参加的先决条件。 该研讨会是专为研究生，博士后研究人员和教师在计算生物物理学和物理有机化学谁有一些经验与计算化学方法，并寻求提高他们的能力，包括酶反应的建模。鼓励参与者在研讨会期间讨论和研究自己的研究中的生物分子系统。