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Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM): Supporting the software infrastructure for cryoEM techniques.

电子冷冻显微镜协作计算项目 (CCP-EM)：支持冷冻电子显微镜技术的软件基础设施。

基本信息

批准号：
MR/N009614/1
负责人：
Martyn Winn
金额：
$ 139.08万
依托单位：
Science and Technology Facilities Council
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2016
资助国家：
英国
起止时间：
2016 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=MR%2FN009614%2F1
关键词：
Collaborative Computational Project Electron cryo

项目摘要

Understanding how biological molecules function inside cells is vital to combating disease. While experimental techniques such as macromolecular crystallography and nuclear magnetic resonance spectroscopy have for many years given detailed information on important molecules in the cell, attention is now moving to how these molecules interact with each other and how they are affected by their location in the cell. Electron cryo-Microscopy (cryo-EM) provides very useful information here, and bridges the gap between individual molecules and the whole cell. In the most favourable cases, detailed images of assemblies of molecules can be obtained, while at lower resolutions electron tomograms can show internal molecular details from within intact parts of cells or tissues. Advances in instrumentation and data processing have led to a significant increase in the application of cryo-EM in recent years, such that it is now one of the most important experimental techniques available in structural and cellular biology. To exploit fully cryo-EM requires good software for processing the primary experimental data and for interpretating it in terms of molecular or cellular structure. However, software provision is patchy and fragmented, and individual labs face a steep learning curve when trying to create a suitable software environment for their projects. The macromolecular crystallography community faced such a challenge more than 30 years ago, and the Collaborative Computational Project No. 4 (CCP4) was created to address this challenge. In the years following, CCP4 has grown to be a major international project, and has underpinned many of the advances in our understanding of cells at the molecular level. In the last 10 years, similar collaborative projects for structural biology have been created: CCPN for nuclear magnetic resonance spectroscopy, CCPBioSim for biomolecular simulation, and CCP-SAS for small angle X-ray and neutron scattering. In response to the growing scientific role of cryoEM, we have recently created the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM).There are at least 25 groups in the UK active in the field of cryo-EM, with a rapidly increasing number of crystallography groups looking to obtain complementary information from cryoEM. CCP-EM is open to all these groups, and will coordinate efforts within the UK community. It will support users through dissemination of information on available software, helpdesk support, and directed training. It will support developers through technical help and by helping to distribute their software to the community. CCP-EM is also developing its own software suite for processing cryoEM data by integrating existing programmes into a robust and user-friendly framework. The creation of CCP-EM was facilitated by the award of a Partnership Grant, and we now seek a follow-on Partnership Grant to support the collaborative project as it matures and expands. While the first grant focussed on single particle techniques, wherein individual molecules or complexes are imaged, we now proposed to expand the scope to electron tomography which provides in situ imaging of complexes and larger structures in the cell.A continuation of CCP-EM will lead to a better use of software within UK groups. The support of a dedicated group of scientists will greatly speed up the process of establishing new groups or helping established microscopists move into new areas (such as tomography). CCP-EM will directly support the new national EM facility on the Harwell Campus, helping users get the most from a new resource. However, the most important output is the development of a community spirit, that encourages individual scientists to pool their efforts. The creation of scientific communities in the UK leads to the best use of public money, and maximises the return on the UK's investment in microscopy facilities

了解生物分子如何在细胞内发挥作用对于对抗疾病至关重要。虽然实验技术，如大分子晶体学和核磁共振光谱学多年来已经给出了细胞中重要分子的详细信息，但现在注意力正在转移到这些分子如何相互作用以及它们在细胞中的位置如何影响它们。冷冻电子显微镜（cryo-EM）提供了非常有用的信息，并在单个分子和整个细胞之间架起了差距的桥梁。在最有利的情况下，可以获得分子组装的详细图像，而在较低分辨率下，电子断层摄影可以显示来自细胞或组织的完整部分内的内部分子细节。近年来，仪器和数据处理的进步导致cryo-EM的应用显着增加，因此它现在是结构和细胞生物学中最重要的实验技术之一。为了充分利用冷冻EM需要良好的软件来处理主要的实验数据，并解释它的分子或细胞结构。然而，软件供应是不完整和分散的，并且当尝试为其项目创建合适的软件环境时，单个实验室面临着陡峭的学习曲线。大分子晶体学界在30多年前就面临着这样的挑战，为了应对这一挑战，创建了第4号合作计算项目（CCP 4）。在接下来的几年里，CCP 4已经发展成为一个重要的国际项目，并支持了我们在分子水平上理解细胞的许多进展。在过去的10年中，类似的结构生物学合作项目已经创建：CCPN用于核磁共振光谱，CCPBioSim用于生物分子模拟，CCP-SAS用于小角度X射线和中子散射。为了应对cryoEM日益增长的科学作用，我们最近创建了电子冷冻显微镜合作计算项目（CCP-EM）。英国至少有25个团体活跃在cryo-EM领域，同时，越来越多的晶体学团体希望从cryoEM中获得补充信息。CCP-EM对所有这些团体开放，并将协调英国社区内的努力。它将通过传播关于现有软件的信息、服务台支助和有针对性的培训来支助用户。它将通过技术帮助和帮助向社区分发软件来支持开发人员。CCP-EM还正在开发自己的软件套件，通过将现有程序整合到一个强大和用户友好的框架中来处理cryoEM数据。CCP-EM的创建得到了伙伴关系赠款的推动，我们现在寻求后续伙伴关系赠款，以支持合作项目的成熟和扩展。虽然第一笔资助集中在单粒子技术上，其中对单个分子或复合物进行成像，但我们现在提议将范围扩大到电子断层扫描，为细胞中的复合物和较大结构提供原位成像。CCP-EM的继续将导致英国团队更好地使用软件。一个专门的科学家小组的支持将大大加快建立新小组的过程，或帮助建立显微镜进入新的领域（如断层扫描）。CCP-EM将直接支持Harwell校园的新国家EM设施，帮助用户从新资源中获得最大收益。然而，最重要的成果是发展了一种社区精神，鼓励科学家个人共同努力。在英国创建科学社区可以最好地利用公共资金，并最大限度地提高英国在显微镜设施方面的投资回报