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

了解生物分子在细胞内如何发挥作用对于对抗疾病至关重要。虽然大分子晶体学和核磁共振波谱等实验技术多年来已经提供了细胞中重要分子的详细信息，但现在人们的注意力转向这些分子如何相互作用以及它们在细胞中的位置如何受到影响。冷冻电子显微镜（cryo-EM）在这里提供了非常有用的信息，并弥合了单个分子和整个细胞之间的差距。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，电子断层扫描可以显示细胞或组织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冷冻电镜的应用显着增加，使其成为结构和细胞生物学中最重要的实验技术之一。要充分利用冷冻电镜，需要良好的软件来处理主要实验数据并根据分子或细胞结构对其进行解释。然而，软件供应是零散且分散的，各个实验室在尝试为其项目创建合适的软件环境时面临着陡峭的学习曲线。 30多年前，高分子晶体学界就面临着这样的挑战，协作计算项目4号（CCP4）就是为了应对这一挑战而创建的。在接下来的几年里，CCP4 已发展成为一个重要的国际项目，并支撑了我们在分子水平上理解细胞的许多进展。在过去的 10 年里，类似的结构生物学合作项目已经创建：用于核磁共振波谱的 CCPN、用于生物分子模拟的 CCPBioSim 以及用于小角度 X 射线和中子散射的 CCP-SAS。为了应对冷冻电镜日益增长的科学作用，我们最近创建了电子冷冻显微镜协作计算项目 (CCP-EM)。英国至少有 25 个团体活跃在冷冻电镜领域，并且迅速发展越来越多的晶体学团体希望从冷冻电镜中获取补充信息。 CCP-EM 对所有这些团体开放，并将协调英国社区内的努力。它将通过传播有关可用软件、帮助台支持和定向培训的信息来为用户提供支持。它将通过技术帮助和帮助向社区分发他们的软件来支持开发人员。 CCP-EM 还正在开发自己的软件套件，通过将现有程序集成到强大且用户友好的框架中来处理冷冻电镜数据。合作伙伴赠款的授予促进了 CCP-EM 的创建，我们现在寻求后续合作伙伴赠款，以支持该合作项目的成熟和扩展。虽然第一笔资助主要集中在对单个分子或复合物进行成像的单粒子技术，但我们现在建议将范围扩大到电子断层扫描，它可以对细胞中的复合物和较大结构进行原位成像。CCP-EM 的延续将导致以便在英国团体内更好地使用软件。专门的科学家小组的支持将大大加快建立新小组或帮助现有显微镜专家进入新领域（例如断层扫描）的过程。 CCP-EM 将直接支持哈韦尔校区新的国家 EM 设施，帮助用户从新资源中获得最大收益。然而，最重要的成果是社区精神的发展，鼓励个体科学家共同努力。英国科学界的创建可以充分利用公共资金，并最大限度地提高英国在显微镜设施上的投资回报

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Cryo-EM structure of a microtubule-bound parasite kinesin motor and implications for its mechanism and inhibition.

微管结合寄生虫驱动蛋白马达的冷冻电镜结构及其机制和抑制的意义。

DOI：
http://dx.10.1016/j.jbc.2021.101063
发表时间：
2021
期刊：
The Journal of biological chemistry
影响因子：
0
作者：
Cook AD
通讯作者：
Cook AD

Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry.

Jwalk 和 MNXL Web 服务器：使用交联质谱的限制进行模型验证。

DOI：
http://dx.10.1093/bioinformatics/bty366
发表时间：
2018
期刊：
Bioinformatics (Oxford, England)
影响因子：
0
作者：
Bullock JMA
通讯作者：
Bullock JMA

Cryo-EM targets in CASP14.

CASP14 中的冷冻电镜目标。

DOI：
http://dx.10.1002/prot.26216
发表时间：
2021
期刊：
Proteins
影响因子：
2.9
作者：
Cragnolini T
通讯作者：
Cragnolini T

TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows.

TEMPy2：一个 Python 库，具有改进的 3D 电子显微镜密度拟合和验证工作流程。

DOI：
http://dx.10.1107/s2059798320014928
发表时间：
2021
期刊：
Acta crystallographica. Section D, Structural biology
影响因子：
0
作者：
Cragnolini T
通讯作者：
Cragnolini T

Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM.

使用 Buccaneer 和 CCP-EM 将自动模型构建到冷冻电镜图谱中的当前方法。

DOI：
http://dx.10.1107/s2059798320005513
发表时间：
2020
期刊：
Acta crystallographica. Section D, Structural biology
影响因子：
0
作者：
Hoh SW
通讯作者：
Hoh SW

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Martyn Winn其他文献

BIROn - Birkbeck Institutional Research Online

BIROn - 伯贝克学院在线研究

DOI：
10.1093/nar/gkp1078
发表时间：
2024-09-13
期刊：
Nucleic Acids Research
影响因子：
14.9
作者：
Chris Wood;T. Burnley;A. Patwardhan;S. Scheres;Maya Topf;Alan Roseman;Martyn Winn
通讯作者：
Martyn Winn