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

• 批准号: 10400939
• 负责人: PAUL David ADAMS
• 金额: $ 154.51万
• 依托单位: UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
• 依托单位国家: 美国
• 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/10400939
• 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

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：为晶体学研究社区提供高质量的软件， cryo-EM 大分子结构的知识，即原子如何在空间中排列，以及如何在空间中排列。 他们改变形状随着时间的推移或响应外部因素，有必要了解他们的 功能这些信息也经常被用来帮助开发新的治疗方法。 晶体学和电子低温显微镜（cryo-EM）是测定三种晶体结构的有效方法， 三维大分子结构在Protein Data提供的160，000多个3D结构中， 使用晶体学或冷冻电镜方法已经获得了超过150，000个样品。在 在这两种情况下，实验数据的分析都是一个复杂的计算问题，依赖于 复杂的软件Phenix是一个软件套件，它使用来自X射线衍射的简化数据， 电子衍射、中子衍射或冷冻EM 3D重建来确定大分子 在过去的15年里，它已被广泛使用。Phenix软件和相关的 外联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证词的分析，我们观察到， 资源具有很高的影响力，而且这种影响力正在增长，这是通过增加研究人员的需求和使用来衡量的。 Phenix在支持美国NIH资助的研究方面也发挥着非常重要的作用。因此，我们认为， 我们正式建立凤凰资源，这将：a）支持持续的维护， 优化代码库，以确保它与当前的计算范式和科学 数据标准，B）提高程序可用性和与其他社区软件资源的集成， c）维护软件和硬件基础设施，以便广泛、有效地传播资源， 和d）开展外联、培训和用户支持，以帮助发展受过培训的社区， 能充分利用Phenix软件的研究人员。