METHODS AND APPLICATIONS OF HYBRID QC/MM SIMULATIONS TO BIOMOLECULAR SYSTEMS

生物分子系统混合 QC/MM 模拟的方法和应用

• 批准号: 8364395
• 负责人: TROY WYMORE
• 金额: $ 0.1万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364395
• 关键词: Biochemical Reaction; Biomedical Research; Biophysics; Chemicals; Educational workshop; Enzymes; Faculty; Funding; Grant; High Performance Computing; Hybrids; Methods; Modeling; Molecular; National Center for Research Resources; Organic Chemistry; Participant; Postdoctoral Fellow; Potential Energy; Principal Investigator; Reaction; Research; Research Infrastructure; Research Personnel; Resources; Source; Structure-Activity Relationship; System; Techniques; United States National Institutes of Health; Work; computational chemistry; cost; design; experience; graduate student; high end computer; lectures; molecular mechanics; molecular orbital; quantum; simulation

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The workshop will present computational approaches for the simulation of enzymatic reactions. Lectures will be held on the relevant theoretical background including the applicability of Quantum Chemical (QC) methods for large molecules, re-parameterization of Semiempirical Molecular Orbital (SMO) methods for specific reactions, molecular mechanics (MM) force fields, hybrid QC/MM potential energy functions and simulation techniques on high performance computers. In-depth tutorials will be presented primarily with the use of the freely available pDynamo package developed in the lab of Dr. Martin J. Field and will also include developing SMO parameters for quantitatively accurate enzyme reaction simulations, the issues involved in constructing a QC/MM model and the various methods for generating energy profiles of bio-molecular reactions to determine mechanisms and structure-function relationships. Experience with pDynamo 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 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 bio-molecular systems from their own research during the workshop. Space is limited. This workshop is supported by the NIH-National Center for Research Resources.

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 研讨会将介绍模拟酶反应的计算方法。讲座将围绕相关的理论背景进行，包括大分子量子化学(QC)方法的适用性、特定反应的半经验分子轨道(SMO)方法的重新参数化、分子力学(MM)力场、QC/MM混合势能函数以及在高性能计算机上的模拟技术。深入的教程将主要使用马丁·J·菲尔德博士的实验室开发的免费提供的pDynamo软件包，还将包括为定量准确的酶反应模拟开发SMO参数，构建QC/MM模型所涉及的问题，以及生成生物分子反应能量谱以确定机理和结构-功能关系的各种方法。有pDynamo的经验是有帮助的，但不是出席的先决条件。 该研讨会是为计算生物物理学和物理有机化学方面的研究生、博士后研究人员和教职员工设计的，他们有计算化学方法的经验，并寻求提高他们的能力，包括酶反应的建模。鼓励与会者在研讨会期间根据自己的研究讨论和研究生物分子系统。空间是有限的。 这次研讨会得到了美国国立卫生研究院-国家研究资源中心的支持。