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.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 该研讨会将介绍用于模拟酶促反应的计算方法。讲座将在相关的理论背景下举行，包括用于大分子的量子化学方法（QC）方法的适用性，对特定反应的半符合性分子轨道（SMO）方法的重新参数化，分子力学（MM）力场，混合QC/MM势能功能和模拟技术上的高性能计算机上的QC/MM势能功能和模拟技术。深入的教程将主要使用在Martin J. Field博士实验室中开发的自由使用的PDYNAMO软件包，还将包括开发SMO参数以定量准确的酶反应模拟，构建QC/MM模型中涉及的问题以及为生成Bio-Molecoleculace Reactions的各种方法以确定机制和结构的方法和结构的方法。 PDYNAMO的经验很有帮助，但不是出席的先决条件。 该研讨会专为研究生，博士后研究人员和计算生物物理学和物理有机化学的教师设计，他们具有计算化学方法的经验，并试图增强其能力以包括酶促反应的建模。鼓励参与者在研讨会期间从自己的研究中讨论和研究生物分子系统。空间有限。 该研讨会得到了美国国家航空航天局研究资源中心的支持。