Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.
Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.
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DOI：
10.1007/s10969-008-9045-8
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发表时间：
2009-03
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影响因子：
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通讯作者：
Richardson, Jane S
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作者：
Headd, Jeffrey J;Immormino, Robert M;Keedy, Daniel A;Emsley, Paul;Richardson, David C;Richardson, Jane S
蛋白质晶体结构中的错配侧链是利用这些结构指导进一步科学推断的绊脚石。由于表面无序和低电子密度引起的问题很难解决，但是即使在有序的区域，也会出现大量的系统误差，导致侧链以可预测的方式向后适应局部密度。MolProbity网站在诊断此类错误方面非常有效，并且可以使用全原子接触和氢键网络，对Asn或Gln侧链酰胺180°翻转等少数特殊情况进行可靠的自动纠正。然而，大多数危险残基涉及四面体几何，其有效校正需要严格评估侧链运动和有时骨干移位。目前的工作将鲁棒自动校正的好处扩展到更多侧链类型。Autofix方法使用MolProbity质量统计来识别Leu， Thr， Val和Arg中的候选系统翻转误差，在Coot中使用转子选择的实空间改进提出校正位置，并根据MolProbity标准的改进和χ角的变化接受或拒绝校正。标准的选择是保守的，在检查了许多单独的结果之后，以确保有效的修正。为了测试该方法，运行Autofix并分析了945个具有代表性的PDB文件和文件1YHQ的50S核糖体亚基。超过40%的Leu、Val和Thr异常值和15%的Arg异常值被成功校正，总共校正了3,679个侧链，平均每个结构4个侧链。蛋白质晶体结构中常见的一类错配侧链是由于将侧链向后放置到局部电子密度中的系统误差造成的。一种名为“Autofix”的全自动方法可以识别Leu， Val， Thr和Arg的此类错误，并使用MolProbity验证标准和Coot转子的实时空间细化来纠正超过三分之一的错误。本文的在线版本（doi:10.1007/s10969-008-9045-8）包含补充材料，仅供授权用户使用。
Misfit sidechains in protein crystal structures are a stumbling block in using those structures to direct further scientific inference. Problems due to surface disorder and poor electron density are very difficult to address, but a large class of systematic errors are quite common even in well-ordered regions, resulting in sidechains fit backwards into local density in predictable ways. The MolProbity web site is effective at diagnosing such errors, and can perform reliable automated correction of a few special cases such as 180° flips of Asn or Gln sidechain amides, using all-atom contacts and H-bond networks. However, most at-risk residues involve tetrahedral geometry, and their valid correction requires rigorous evaluation of sidechain movement and sometimes backbone shift. The current work extends the benefits of robust automated correction to more sidechain types. The Autofix method identifies candidate systematic, flipped-over errors in Leu, Thr, Val, and Arg using MolProbity quality statistics, proposes a corrected position using real-space refinement with rotamer selection in Coot, and accepts or rejects the correction based on improvement in MolProbity criteria and on χ angle change. Criteria are chosen conservatively, after examining many individual results, to ensure valid correction. To test this method, Autofix was run and analyzed for 945 representative PDB files and on the 50S ribosomal subunit of file 1YHQ. Over 40% of Leu, Val, and Thr outliers and 15% of Arg outliers were successfully corrected, resulting in a total of 3,679 corrected sidechains, or 4 per structure on average. Summary Sentences: A common class of misfit sidechains in protein crystal structures is due to systematic errors that place the sidechain backwards into the local electron density. A fully automated method called “Autofix” identifies such errors for Leu, Val, Thr, and Arg and corrects over one third of them, using MolProbity validation criteria and Coot real-space refinement of rotamers. The online version of this article (doi:10.1007/s10969-008-9045-8) contains supplementary material, which is available to authorized users.