Automated protein model building with flexible models and high resolution data

将原子模型构建到电子密度图中是通过X射线或EM方法求解3D结构的关键阶段。这项任务曾经很耗时，现在通过Cowtan博士的“Buccaneer”软件（700次引用）等软件包实现了自动化。Buccaneer在数据分辨率较低时显示出一流的性能，但在分辨率较好时，它的性能不如竞争软件，并且生成的模型需要更多的手动调整。其优点和缺点都来自于蛋白质的过于刚性的模型，目的是引入（a）一种新的用于高分辨率电子密度的特征识别方法，以及（B）一种更灵活的蛋白质骨架和侧链构象模型。当数据分辨率良好时，两者都有助于提高性能，而后者将减少在中间分辨率下模型所需的手动调整量。Buccaneer软件的独特之处在于它由电子密度的形状而不是峰值驱动。这种方法是低分辨率性能的关键，但尚未用于高分辨率数据。此外，在更高的分辨率下，还可以优化交互式图形使用的方法。X射线晶体结构解决方案越来越多地由非专业人员进行，他们通常依靠软件来产生精确的结构，而手动验证有限。因此，软件在不依赖人工调整的情况下产生最完整和最准确的模型变得越来越重要。通过从已知的高分辨率结构中挖掘电子密度数据，开发一种新的特征识别功能，并对现有的搜索算法进行优化。现有的测试结构将用于确定模型的局限性，以改进模型参数化。新的功能将在两个现有的电脑软件包，'海盗'和'酷'。这项工作涉及编程和数据分析，这两者都是高度可转移的技能。从工作中产生的出版物很可能被软件用户高度引用，这将为未来的研究生涯奠定基础。

Building an atomic model into an electron density map is a key stage in the solution of 3D structures by X-ray or EM methods. Once time consuming, this task is now automated by packages such as Dr Cowtan's 'Buccaneer' software (700 citations). Buccaneer shows class leading performance when data resolution is poor, however it performs less well than competing software when resolution is good and the resulting models require more manual tweaking. Both the strengths and weaknesses arise from an over-rigid model of the protein.The aim is to introduce (a) a new feature recognition method for use with high resolution electron density, and (b) a more flexible model of both the protein backbone and of sidechain conformations. Both will contribute to improved performance when data resolution is good, and the latter will reduce the amount of manual tuning required to the model at intermediate resolutions.The Buccaneer software is unique in that it is driven by the shape of the electron density rather than the peak values. This approach was key to lower resolution performance, but has yet to be exploited for high resolution data. Furthermore at higher resolution there is the possibility of optimizing the method for interactive graphical use.X-ray crystallographic structure solution is increasingly being conducted by non-specialists, who often rely on software to produce an accurate structure with limited manual validation. As a result it is increasingly important that the software produce the most complete and accurate model possible without relying on manual tuning.A new feature recognition function will be developed by data-mining electron density from known high resolution structures, with an optimized version of an existing search algorithm. Existing test structures will be used to identify model limitations for the implementation of improvements to model parameterization. The new features will be implement into two existing computer software packages, 'buccaneer' and 'coot'. The work involves programming and data analysis, both of which are highly transferable skills. Publications arising from the work are likely to be highly cited by software users, which will provide a foundation for a future research career.