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：向研究社区提供高质量的软件，以进行晶体学和 冷冻em 了解大分子的结构，即原子如何在太空中排列以及如何 它们随着时间的推移或对外部因素的响应而改变形状，必须 功能。该信息还经常被利用，以帮助开发新的治疗剂。 晶体学和电子冷冻微镜（Cryo-EM）是确定三个的强大方法 尺寸大分子结构。在蛋白质数据上可用的160,000+ 3D结构中 使用晶体学或冷冻EM方法到达了15万多个银行。在 两种情况下，对实验数据的分析都是一个依赖的计算复杂问题 复杂的软件。 Phenix是一个软件套件，使用X射线衍射中减少的数据， 电子衍射，中子衍射或冷冻EM 3D重建，以确定大分子 在过去15年中，结构已被广泛使用。 Phenix软件和相关的 外展和培训等活动已成为国家和国际资源。 基于对出版物，专利和WWPDB沉积的分析，我们观察到phenix 资源具有很大的影响，并且通过增加的研究人员需求和使用来衡量，这正在增长。 Phenix在支持美国境内的NIH资助研究方面还起着非常重要的作用。所以， 我们正式建立了苯金公司资源，该资源将：a）支持持续的维护和 优化代码库，以确保它与当前的计算范式和科学相关 数据标准，b）改善计划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架构，以进行广泛，有效的资源传播， d）进行外展，培训和用户支持，以帮助发展受过训练的社区 可以充分利用Phenix软件的研究人员。