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及其在改进蛋白质结构测定中的应用，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在方法上的突破，该突破允许分子相互作用的空间细节的可视化和定量，包括所有显式氢原子。当两个原子在0.5埃的接触范围内时，可视化产生两个斑点表面；定量分数对于氢键和范德华接触为正项，对于不利重叠为负项，在表面局部评估。我们已经制作了一个改进的旋转体库和工具来显示晶体学重建程序中的全原子接触和电子密度，它可以灵敏地检测任何拟合误差。这个项目的理论部分将努力调和这里看到的高水平的包装特异性与标准的基于能量的模型的预测。所应用的组分将利用该技术提供的独立新信息（不包括在当前的精化程序中）来加速和提高结构测定的准确性：自动纠正酰胺翻转和其他系统错误；纳入改进的循环库；自动化侧链装配，包括替代构象；开发更好的搜索策略，优化侧链和肽翻转，旋转体的选择，并在细化协调运动；改进对c - α周围键角畸变的处理；开发方便的全原子验证工具。通过将这些技术的自动化版本顺利集成到用于结构基因组学工作的模型构建、改进和验证阶段的系统中，将特别强调对高通量晶体学的需求。

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.