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

该项目的研究人员寻求开发和改进将在高性能超级计算机上运行的软件工具，以寻找新的埃博拉病毒抗体样剂，这些抗体类试剂将发出埃博拉病毒在感染者身上存在的信号。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、廉价和准确地检测唾液中的病毒。其目标是开发一种高度敏感的测试，可以用于尚未表现出任何症状的患者。该项目的结果可以为未感染的患者节省目前实施的为期3周的隔离的情感负担和费用。及早发现也可能大大提高埃博拉患者的存活率。这项关键的工作将满足国家应对埃博拉病毒的关键和迫切需要。该提案中描述的项目旨在通过提议团队所做的分子动态模拟来识别具有所需动态特性的抗体样蛋白。这些动力学性质是在原子水平上的，将通过对Blue Waters进行全原子千万亿级MD计算机模拟来获得。提出建议的团队将在实验周期中充当关键中间人。他们将采用宾夕法尼亚州立大学白蛋白设计团队开发的潜在抗体，通过千万亿级模拟识别白蛋白的动态特征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分校的生物传感器实验室，该实验室将设计和制造该工具。由于建模和模拟将是两端科学家的合作成果，提议团队还将建立一个远程可视化工具，供科学家在实验中进行协作。

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.