Phenix: Integrated algorithms for high quality models from crystallographic and cryo-EM data

摘要/Abstract Phenix软件的开发是4个小组高度合作的结果 位于劳伦斯伯克利实验室，洛斯阿拉莫斯国家实验室，剑桥大学， 杜克大学。在我们先前工作的基础上，我们将继续合作开发新的 改进结构解决方案的方法，重点是低（近原子）分辨率（3- 4.5 μ m）。 研究人员仍然遇到重大问题，解决和完成结构，在这一制度。 单波长异常（SAD）定相、分子置换、模型构建的改进， 改进和验证将使研究人员有可能解决更具挑战性的实验， 系统.这是特别及时的，因为新的数据收集方法，如连续晶体学， 正在产生较低分辨率的膜蛋白结构和大的柔性复合物。 单粒子低温电子显微镜（cryo-EM）领域的最新发展产生了 一个快速增长的大分子复合物的数量解决从头开始。因此 凤凰团队在未来5年的重要发展领域将是冷冻EM，特别是 近原子分辨率单粒子图像重建。这是最令人兴奋的 近年来结构生物学领域的发展。我们的目标将是合作， 我们目前的方法，并开发新的方法，以解决模型拟合，模型构建， 原子模型的改进和验证来自低温EM地图。

Overall Summary/Abstract The Phenix software has been developed as a result of the highly collaborative work of 4 groups located at Lawrence Berkeley Laboratory, Los Alamos National Laboratory, Cambridge University, and Duke University. Building on our prior work we will continue to collaborate in the development of new methods to improve structure solution, with a focus on low (near atomic) resolution (3-4.5Å). Researchers still encounter significant problems in solving and completing structures in this regime. Improvements in single wavelength anomalous (SAD) phasing, molecular replacement, model building, refinement and validation will make it possible for researchers to tackle more challenging experimental systems. This is particularly timely as new approaches to data collection, such as serial crystallography, are producing lower resolution structures of membrane proteins and large flexible complexes. Recent developments in the field of single particle cryo-electron microscopy (cryo-EM) have generated a rapid growth in the number of large macromolecular complexes solved ab initio. Therefore, a significant area of development for the Phenix team in the next 5 years will be cryo-EM, in particular near atomic resolution single particle image reconstruction. This is one of the most exciting developments in the field of structural biology in recent history. Our goal will be to collaborate to extend our current methods, and develop new ones, to address the problems of model fitting, model building, refinement and validation of atomic models derived from cryo-EM maps.