Dept of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.
RIKEN Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo, 103-0027, Japan.
Nat Commun. 2020 Dec 18;11(1):6321. doi: 10.1038/s41467-020-20177-1.
We present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using: structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.
我们提出了一种测量 NMR 蛋白质结构准确性的方法。它将随机卷曲指数 [RCI] 与通过数学刚性理论预测的局部刚性进行比较，该理论是从 NMR 结构 [FIRST] 计算得出的，使用相关分数（评估二级结构）和 RMSD 分数（衡量整体刚性）。我们使用以下方法测试其性能：在明确定义的溶剂中进行细化的结构，其质量远优于未细化的结构；为 89 个 NMR 结构生成的诱饵结构；以及准确性的常规预测因子，例如每个残基的约束数、约束违反、结构能量、整体 RMSD、Ramachandran 分布和 clashscore。约束违反和 RMSD 是准确性的糟糕衡量标准。NMR 与晶体结构的比较表明，二级结构同样准确，但晶体结构在环中通常过于刚性，而 NMR 结构通常整体过于松软。我们表明，该方法是对现有准确性衡量标准的有益补充。
