All-Atom Contact Analysis In Improving Structure Quality

该项目的总体目标是进一步发展全原子接触分析，并将其应用于提高蛋白质结构测定的水平，特别是强调结构基因组学所需的自动化。该项目利用了该实验室最近的一项方法学突破，允许对分子相互作用的立体细节进行可视化和量化，包括所有明确的H原子。可视化生成两个原子在0.5埃接触单位内的两个点表面的补丁；定量分数具有表示氢键和范德华接触的正项和表示不利重叠的负项，在表面上进行局部评估。我们已经生产了一个改进的旋转体文库和工具，可以在晶体重建程序中显示全原子接触和电子密度，可以灵敏地检测任何拟合错误。该项目的理论部分将致力于使此处所见的高水平的堆积特性与标准基于能量的模型的预测相一致。所应用的组件将利用这项技术提供的独立的新信息(未包括在当前的精炼程序中)，通过以下方式加快和提高结构确定的准确性：自动校正酰胺翻转和其他系统错误；纳入改进的环库；自动进行侧链拟合，包括替代构象；开发更好的搜索策略，用于优化侧链和肽翻转、旋转体选择以及精炼过程中的协调运动；改进对C-α周围键角扭曲的处理；以及开发方便的全原子验证工具。将特别强调高通量结晶学的需求，将这些技术的自动化版本顺利地集成到用于结构基因组学工作的建模、精炼和验证阶段的系统中。

The overall goal of this project is further development of all-atom contact analysis and its application to the improvement of protein structure determination, especially emphasizing automation needed for structural genomics. The project makes use of a recent methodological breakthrough by this laboratory which allows both visualization and quantitation of the steric details of molecular interaction, including all explicit H atoms. The visualization produces two patches of dot surface wherever two atoms are within 0.5Angstrom units of contact; the quantitative score has positive terms for H-bonds and van der Waals contact and negative terms for unfavorable overlap, evaluated locally on the surface. We have already produced an improved rotamer library and tools to display all- atom contacts along with electron density in crystallographic rebuilding programs, which can sensitively detect any fitting errors. The theoretical component of this project will work to reconcile the high level of packing specificity seen here with the predictions of standard energy-based models. The applied component will utilize the independent new information provided by this technique (not included in current refinement procedures) both to speed up and to improve the accuracy of structure determination by: automatically correcting amide flips and other systematic errors; incorporating improved loop libraries; automating sidechain fitting, including alternate conformations; developing better search strategies for optimizing sidechain and peptide flips, rotamer choices, and concerted motions during refinement; improving treatment of bond angle distortions around C-alphas; and developing convenient all-atom validation tools. Particular emphasis will be given to the needs of high-throughput crystallography, by smoothly integrating automated versions of these techniques into the systems used for the model-building, refinement, and validation stages of structural genomics work.