Phenix: providing high quality software to the research community for crystallography and cryo-EM

Phenix：为晶体学和冷冻电镜研究界提供高质量软件

基本信息

批准号：
10194082
负责人：
PAUL David ADAMS
金额：
$ 129.71万
依托单位：
UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-05-03 至 2026-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10194082
关键词：
3-Dimensional Address Adherence Awareness Biological Chemicals Code Communities Complex Computer software Cryoelectron Microscopy Crystallography Data Data Analyses Data Science Data Set Deposition Development Education and Outreach Educational workshop Ensure Environment Event Experimental Models FAIR principles Funding Goals Health Human Infrastructure International Knowledge Language Legal patent Libraries Life Maintenance Measures Methods Modeling Modernization Modification Molecular Structure Monoclonal Antibody R24 National Institute of General Medical Sciences Neutron Diffraction Online Systems Play Program Research Project Grants Publications Pythons Research Research Personnel Research Support Resources Role Schools Scientist Shapes Software Tools Structure System Techniques Testing Therapeutic Time Training Training Support United States National Institutes of Health Update Videoconferencing Visualization Work Writing X ray diffraction analysis X-Ray Crystallography base biological systems data standards electron diffraction experimental analysis graphical user interface human disease improved large datasets literature citation macromolecule novel therapeutics open source operation outreach programs protein data bank rapid growth reconstruction response structural biology symposium three dimensional structure tool uptake usability web site

项目摘要

Phenix: providing high quality software to the research community for crystallography and cryo-EM Knowledge of the structure of macromolecules, i.e. how the atoms are arranged in space and also how they change shape over time or in response to external factors, is necessary to understand their function. This information is also routinely exploited to aid in the development of new therapeutics. Crystallography and electron cryo-microscopy (cryo-EM) are powerful methods for determining three- dimensional macromolecular structures. Of the 160,000+ 3D structures available at the Protein Data Bank more than 150,000 have been arrived at using either crystallographic or cryo-EM methods. In both cases, the analysis of the experimental data is a computationally complex problem that relies on sophisticated software. Phenix is a software suite that uses reduced data from X-ray diffraction, electron diffraction, neutron diffraction or cryo-EM 3D reconstructions to determine macromolecular structures and has become widely used over the past 15 years. The Phenix software and associated activities such as outreach and training have become a national and international resource. Based on an analysis of publications, patents, and wwPDB depositions we observe that Phenix resource is of high impact and this is growing, as measured by increasing researcher demand and use. Phenix also plays a very significant role in supporting NIH funded research within the US. Therefore, we formally establish the Phenix Resource, which will: a) support the continued maintenance and optimization the code base to ensure that it keeps pace with current computing paradigms and scientific data standards, b) improve program usability and integration with other community software resources, c) maintain the software and hardware infrastructure for broad, efficient dissemination of the resource, and d) undertake outreach, training and user support to help grow the community of trained researchers who can make best use of the Phenix software.

Phenix：为晶体学研究界提供高质量的软件冷冻电镜有关大分子结构的知识，即原子如何在空间中排列以及如何排列它们会随着时间的推移或对外部因素的反应而改变形状，因此有必要了解它们的形状功能。这些信息也经常被用来帮助开发新疗法。晶体学和电子冷冻显微镜 (cryo-EM) 是确定三项功能的强大方法。三维大分子结构。 Protein Data 提供 160,000 多个 3D 结构使用晶体学或冷冻电镜方法已获得超过 150,000 个样本库。在在这两种情况下，实验数据的分析都是一个计算复杂的问题，依赖于复杂的软件。 Phenix 是一个软件套件，它使用 X 射线衍射的简化数据，通过电子衍射、中子衍射或冷冻电镜 3D 重建来确定大分子结构并在过去 15 年中得到广泛应用。 Phoenix 软件及相关外展和培训等活动已成为国家和国际资源。根据对出版物、专利和 wwPDB 沉积物的分析，我们观察到 Phenix 资源具有很高的影响力，并且根据研究人员需求和使用的增加来衡量，这种影响力正在不断增长。 Phoenix 在支持美国国立卫生研究院 (NIH) 资助的研究方面也发挥着非常重要的作用。所以，我们正式建立Phenix Resource，它将： a) 支持持续维护和优化代码库，以确保它与当前的计算范例和科学保持同步数据标准，b) 提高程序可用性以及与其他社区软件资源的集成， c) 维护软件和硬件基础设施，以实现资源的广泛、高效传播， d) 开展外展、培训和用户支持，以帮助发展经过培训的社区能够充分利用 Phoenix 软件的研究人员。