Motion-Planning Based Techniques for Modeling & Simulating Molecular Motions

基于运动规划的建模技术

• 批准号: 0830753
• 负责人: Nancy Amato
• 金额: $ 37万
• 依托单位: Texas A&M Engineering Experiment Station
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-15 至 2014-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0830753&HistoricalAwards=false
• 关键词: Motion; Planning; Based; Techniques; Modeling

NUMBER: 0830753INSTITUTION: Texas Engineering Experiment StationPI: Amato, Nancy & Rauchwerger, LawrenceTITLE: Motion-Planning Based Techniques for Modeling & Simulating Molecular MotionsMolecular motions play an essential role in many biochemical processes. Since it is difficult to experimentally observe molecular motions, computational methods for studying such issues are essential. This research investigates a novel computational method for studying molecular motions that the investigators have developed and validated against experimental data in preliminary work. The research has the potential to provide insight into a number of important questions related to protein folding, stability, and solubility. For example, protein misfolding and aggregation is associated with devastating neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, prion diseases, and related diseases. In addition to publications, results generated by the research are shared with the community in a publicly available database of molecular motions. The protein folding server also allows scientists to submit their own proteins which will be analyzed for them: http://parasol.tamu.edu/foldingserver/.The new computational method invested in this research represents a trade-off between methods such as molecular dynamics and Monte Carlo simulations that provide detailed individual folding trajectories and techniques such as statistical mechanical methods that provide global folding landscape statistics. This method builds a graph (roadmap) corresponding to an approximate map of the molecule's energy landscape that encodes many (typically thousands) folding pathways. Though the individual pathways produced are not as detailed as trajectories generated from a molecular dynamics simulation, they can be used to study properties such as secondary structure formation order and folding kinetics. The major research goals of this project include the development of new and/or improved metrics and analysis techniques for conformations and roadmaps that can be applied in protein stability and kinetics studies and the development of strategies for employing high-performance computing to increase the size and complexity of the systems that can be studied. The investigators validate and apply these new techniques to folding core identification, amyloid formation, kinetics studies, and comparative analysis of proteins.

编号：0830753机构：德克萨斯工程实验站：Amato，Nancy＆Rauchwerger，Lawrencetitle：基于运动计划的技术，用于建模和模拟分子运动运动运动在许多生物化学过程中起着至关重要的作用。 由于很难实验观察分子运动，因此研究此类问题的计算方法至关重要。 这项研究研究了一种新的计算方法，用于研究研究者已经根据初步工作中实验数据开发和验证的分子运动。 这项研究有可能洞悉与蛋白质折叠，稳定性和溶解度有关的许多重要问题。 例如，蛋白质错误折叠和聚集与毁灭性神经退行性疾病有关，例如阿尔茨海默氏病，帕金森氏病，prion病和相关疾病。 除出版物外，研究产生的结果在分子动作的公开数据库中与社区共享。 蛋白质折叠服务器还允许科学家提交自己的蛋白质，该蛋白质将对它们进行分析：http：//parasol.tamu.edu/foldingserver/.The...tame http：//parasol.tamu/foldingserver/.Sthie Respart in Tun Reseans投资的新计算方法代表了分子等方法之间的权衡权衡。提供详细的单个折叠轨迹和技术的动力学和蒙特卡洛模拟，例如提供全局折叠景观统计的统计机械方法。 该方法构建了一个图形（路线图），该图对应于分子的能量景观的近似图，该图编码了许多（通常是数千）折叠途径。 尽管所产生的单个途径不像分子动力学模拟产生的轨迹那样详细，但它们可用于研究诸如二级结构形成顺序和折叠动力学之类的属性。 该项目的主要研究目标包括开发新的和/或改进的指标和分析技术，以用于构象和路线图，这些方法可用于蛋白质稳定性和动力学研究，以及采用使用高性能计算来增加规模和增加规模和的策略可以研究的系统的复杂性。 研究人员验证并将这些新技术应用于折叠核心鉴定，淀粉样蛋白形成，动力学研究和蛋白质比较分析。