Novel methodologies for conformational sampling and QM/MM simulations in complex systems

复杂系统中构象采样和 QM/MM 模拟的新方法

• 批准号: 0704036
• 负责人: Mark Tuckerman
• 金额: $ 42.75万
• 依托单位: New York University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2010-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0704036&HistoricalAwards=false
• 关键词: Novel; methodologies; conformational; sampling; QM

Mark E. Tuckerman of New York University is supported by the Theoretical and Computational Chemistry program to develop and implement methods based on specialized variable transformations that are capable of sampling the conformational equilibria of complex systems. This approach reduces the effects of energy barriers without altering thermodynamic and equilibrium properties. Applications of these methods include small peptides as test cases, and fast-folding proteins. A second theme of the research is to develop pseudopotentials appropriate for use in quantum mechanical/molecular mechanical (QM/MM) methods. An initial application of this method is to study the catalytic mechanism of the enzyme histone deacetylase, which is linked to various types of cancer. This work is having a broad impact in developing sampling and search algorithms for bio-simulations. Codes developed in this research, as well as a database of pseudopotentials, are freely available on the PI''s web site. Research results are incorporated into the classroom at the undergraduate and graduate level. Outreach to the community includes non-technical talks to students and faculty at regional middle schools, high school, colleges and universities.

纽约大学的马克·塔克曼（Mark E. 这种方法在不改变热力学和平衡特性的情况下降低了能屏障的影响。 这些方法的应用包括小肽作为测试用例和快速折叠蛋白。 该研究的第二个主题是开发适合用于量子机械/分子机械（QM/mm）方法的伪电势。 该方法的最初应用是研究酶脱乙酰基酶的催化机理，该酶脱乙酰基酶与各种类型的癌症有关。 这项工作在开发采样和搜索算法中对生物模拟产生了广泛的影响。 在本研究中开发的代码以及Pseudopitients的数据库，可以在PI'的网站上免费获得。 研究结果被纳入本科和研究生层面的教室。 向社区的宣传包括与区域中学，高中，大学和大学的学生和教职员工的非技术对话。