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

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。子项目及 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。 研讨会将介绍模拟酶反应的计算方法。讲座将围绕相关理论背景进行，包括量子化学（QC）方法对大分子的适用性、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、混合QC/MM势能函数以及高性能计算机上的模拟技术。深入的教程将主要介绍如何使用 Martin J. Field 博士实验室开发的免费 pDynamo 软件包，还将包括开发用于定量精确酶反应模拟的 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分布以确定机制和结构功能关系的各种方法。使用 pDynamo 的经验很有帮助，但不是参加的先决条件。 该研讨会是为计算生物物理学和物理有机化学领域的研究生、博士后研究人员和教师而设计的，他们拥有计算化学方法的经验，并寻求提高他们的能力，包括酶促反应的建模。鼓励参与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。空间有限。 该研讨会得到了 NIH 国家研究资源中心的支持。

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 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.