RAPID: Development of Rapid In-Field Ebola Infection Screening Guided by Biomolecular Simulation and Collaborative Remote Visualization

RAPID：生物分子模拟和协作远程可视化引导下的快速现场埃博拉感染筛查的发展

• 批准号: 1524703
• 负责人: Zaida Luthey-Schulten
• 金额: $ 20万
• 依托单位: University of Illinois at Urbana-Champaign
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-07-01 至 2017-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1524703&HistoricalAwards=false
• 关键词: RAPID; Development; Rapid; Field; Ebola

The researchers on this project seek to develop and improve software tools, that will run on high-powered supercomputers, in order to find new antibody-like agents for the Ebola virus that will signal the presence of Ebola in an infected person. Once found, effective agents will be incorporated into a diagnostic tool that will be used for rapid, non-invasive, inexpensive and accurate detection of the virus in saliva. The goal is to develop a highly sensitive test that can be used on patients who have not yet shown any symptoms. Results from this project could save uninfected patients the emotional burden as well as the cost of the currently imposed 3-week quarantine. Early detection may also greatly improve the survival rate of Ebola patients. This critical piece of work will meet a key and immediate need in the nation's Ebola response.The project described in this proposal seeks to identify antibody-like proteins with the desired dynamical properties using molecular dynamic simulations done by the proposing team. These dynamical properties are at the atomic level, and will be obtained by performing all-atom petascale MD computer simulations on Blue Waters. The proposing team will serve as a key intermediary in the experiment cycle. They will take potential antibodies developed by an ALB design team at Pennsylvania State University, identify, through petascale simulations, characterize the dynamics of the ALBs and optimize the conformational state change, and provide these results to a bio-sensor laboratory at University of California, Santa Barbara, who will design and build the tool. Since the modelling and simulation will be a collaborative effort with scientists at both ends, the proposing team will also build a remote visualization tool for scientists to collaborate over the experimentation.

该项目的研究人员寻求开发和改进软件工具，这些工具将在高性能超级计算机上运行，以便为埃博拉病毒找到新的抗体样试剂，这将表明埃博拉病毒在感染者中的存在。 一旦发现，有效的试剂将被纳入诊断工具，用于快速，非侵入性，廉价和准确的检测唾液中的病毒。 我们的目标是开发一种高度敏感的测试，可用于尚未出现任何症状的患者。该项目的结果可以为未感染患者节省情感负担以及目前实施的3周隔离的费用。早期发现还可能大大提高埃博拉患者的生存率。 这一关键工作将满足国家埃博拉应对的关键和紧迫需求。该提案中描述的项目旨在使用提案团队完成的分子动力学模拟来识别具有所需动力学特性的抗体样蛋白。这些动力学性质是在原子水平上，并将通过执行所有原子petascale MD计算机模拟蓝色沃茨。提议小组将在试验周期中发挥关键的中介作用。他们将采用宾夕法尼亚州立大学的ALB设计团队开发的潜在抗体，通过千万亿次模拟识别，表征ALB的动力学并优化构象状态变化，并将这些结果提供给加州大学圣巴巴拉的生物传感器实验室，该实验室将设计和构建该工具。由于建模和模拟将是两端科学家的合作努力，提议团队还将为科学家建立一个远程可视化工具，以便在实验中进行合作。