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

Phenix：为结晶学和研究社区提供高质量的软件 冷冻-EM 了解大分子的结构，即原子在空间中如何排列以及如何排列 它们会随着时间的推移或对外部因素的反应而改变形状，这对于理解它们的 功能。这些信息也经常被用来帮助开发新的治疗方法。 结晶学和电子冷冻显微镜(Cryo-EM)是测定三种蛋白质的有效方法。 三维大分子结构。在蛋白质数据网站提供的160,000个3D结构中 已有超过15万人使用结晶学或低温EM方法进行了研究。在……里面 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，它依赖于 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， 用于确定大分子的电子衍射、中子衍射或低温电磁三维重建 结构，在过去的15年里得到了广泛的应用。Phenix软件和相关 外联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证词的分析，我们发现菲尼克斯 资源的影响很大，而且这种影响正在增长，从研究人员需求和使用的增加来衡量。 菲尼克斯还在支持美国国立卫生研究院资助的研究方面发挥着非常重要的作用。因此， 我们正式成立了菲尼克斯资源，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保持同步，并具有科学性 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，以帮助发展训练有素的社区 能够充分利用Phenix软件的研究人员。

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.