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

该子项目是利用 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来源获得主要资金， 因此可以在其他CRISP条目中表示。列出的机构是 中心，不一定是研究者的机构。 该研讨会将提出酶反应模拟的计算方法。讲座将举行相关的理论背景，包括量子化学（QC）方法的适用性大分子，重新参数化的半经验分子轨道（SMO）方法的特定反应，分子力学（MM）力场，混合QC/MM势能函数和高性能计算机上的模拟技术。深入的教程将主要使用在Martin J. Field博士实验室开发的免费提供的pDynamo软件包，还将包括开发用于定量准确的酶反应模拟的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谱以确定机制和结构-功能关系的各种方法。pDynamo的经验是有帮助的，但不是出席的先决条件。 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与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。鼓励参加者在讲习班期间讨论和研究他们自己研究的生物分子系统。空间有限。 本次研讨会由NIH国家研究资源中心支持。

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.