Parallel Software for Fast, Automated Determination of Virus Structures

描述（由申请人提供）：项目摘要电子冷冻显微镜和基于计算机的 3D 图像重建技术正在彻底改变大型复杂生物大分子机器结构的研究方式。这些方法为理解这些机器如何运作提供了关键。我们的目标是在最短的时间内以尽可能高的分辨率可靠地确定病毒结构。这将增强我们了解病毒如何引起各种疾病的能力，并可能为如何最好地开发抗病毒药物提供重要线索。显微镜和图像重建各自带来了一系列重大挑战，而新颖软件的开发显然是我们以及其他人的研究工作成功的关键。我们的目标是大幅增强计算能力，这是我们冷冻重建工作的 3D 结构确定部分的核心。 冷冻重建中所达到的分辨率和解决的结构受到许多因素的限制，其中最重要的是所使用的数值技术。因此，我们将重点关注算法改进，以扩大可研究问题的范围，使达到更高的分辨率成为可能，并缩短解决时间。例如，我们将扩展软件的功能，以检查名义上二十面体病毒的非二十面体成分以及具有较低对称性的粒子。 除了上述改进之外，我们的软件开发兴趣还包括自动化、并行计算和可用性增强。对于许多病毒结构，尤其是大型和/或不对称的病毒结构，图像重建是速率限制步骤。为了减少图像采集和结构确定之间的时间，并缩小新手和专家用户可以达到的分辨率之间的差距，我们将增强 AUTO3DEM，这是我们的自动化系统，用于智能集成图像重建所需的多个应用程序。该系统还提供了一个用于评估新想法的测试平台，并使更广泛的用户可以轻松访问该软件。 拟议的工作应该使我们更接近在显微镜下实时图像重建的目标，或者至少与数据采集紧密结合，以提供快速反馈并快速筛选样品属性。我们的研究还通过与冷冻显微镜、图像处理、数据可视化和解释方面的同事的密切联系、在 NIH、UCSD 和 Agouron 基金会的支持下购买现代显微镜以及与圣地亚哥超级计算机中心的互动而得到很大的利用。我们所有的软件都将可供电子显微镜界轻松访问。 公共卫生相关性：相关性 病毒几乎感染地球上的每一种生物体，导致人类和其他动物严重疾病和死亡，并且还极大地影响食物来源，往往导致饥荒和经济疲软。了解病毒结构为更好地了解病毒如何在易感宿主中复制自身提供了重要的联系。根据透射电子显微镜记录的病毒图像生成的基于计算机的 3D 模型，提供了有关病毒分子结构的重要第一印象。由于获得这些模型所需的时间通常需要数周或数月的专门努力，因此该提案的一个重要目标是将其减少到几小时或几分钟。

DESCRIPTION (provided by applicant): Project Summary Electron cryo-microscopy and computer-based, 3D image reconstruction techniques are revolutionizing the way structures of large, complex biomacromolecular machines are studied. These methods provide keys to understanding how these machines function. Our goal is to determine virus structures reliably at the highest possible resolutions in the shortest amount of time. This will enhance our ability to understand how viruses cause a variety of dieases and may yield important clues about how best to develop anti-viral agents. Microscopy and image reconstruction each pose their own set of significant challenges, and development of novel software clearly represents a key to the success of our research efforts as well as that of others. We aim to substantially enhance the computational capabilities that comprise the heart of the 3D structure determination part of our cryo-reconstruction work. The resolutions achieved and structures solved in cryo-reconstruction are limited by many factors, not the least of which includes the numerical techniques employed. Hence, we will focus on algorithmic improvements that expand the range of problems that can be studied, make it possible to reach higher resolutions, and reduce time to solution. For example, we will extend the capabilities of our software to examine the non-icosahedral components of nominally icosahedral viruses as well as particles with lower symmetries. In addition to the improvements noted above, our software development interests include automation, parallel computing, and enhancements to usability. For many virus structures, especially large and/or asymmetric ones, image reconstruction is the rate limiting step. To reduce the time between image acquisition and structure determination and also narrow the gap between the resolutions that can be reached by novice and expert users, we will enhance AUTO3DEM, our automation system for intelligently integrating the multiple applications required in image reconstruction. This system also provides a test bed for evaluating new ideas and makes the software easily accessible to a wider range of users. The proposed work should take us closer to our goal of real-time image reconstruction at the microscope, or at least tightly coupled to data acquisition, to provide rapid feedback and quickly screen sample properties. Our studies are also heavily leveraged by close ties to colleagues in cryo-microscopy, image processing, and data visualization and interpretation, the acquisition of modern microscopes with support from NIH, UCSD, and the Agouron foundation, and interaction with the San Diego Supercomputer Center. All of our software will be made readily accessible to the electron microscopy community. PUBLIC HEALTH RELEVANCE: Relevance Viruses infect nearly every living organism on Earth, causing serious diseases and death in humans and other animals, and also greatly impact food sources often leading to famine as well as weakened economies. Knowledge of virus structure provides an important link to better understand how viruses replicate themselves in susceptible hosts. Computer-based 3D models generated from virus images recorded in transmission electron microscopes, provide an important, first glimpse about the molecular structures of viruses. As the time required to obtain these models often requires weeks or months of dedicated effort, an important goal of this proposal is to reduce this down to hours or minutes.