A method for validating the accuracy of NMR protein structures.
A method for validating the accuracy of NMR protein structures.
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DOI：
10.1038/s41467-020-20177-1
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发表时间：
2020-12-18
影响因子：
16.6
通讯作者：
Williamson MP
中科院分区：
文献类型：
--
作者：
Fowler NJ;Sljoka A;Williamson MP
我们提出了一种测量核磁共振蛋白结构精度的方法。它将随机线圈指数[RCI]与由核磁共振结构[FIRST]计算的数学刚度理论预测的局部刚度进行比较，使用相关评分（评估二级结构）和RMSD评分（衡量整体刚度）。我们使用在显式溶剂中精炼的结构来测试其性能，这些结构比未精炼的结构要好得多；89个核磁共振结构生成的诱饵结构；以及传统的精度预测指标，如每个残留的约束数、约束违反、结构能量、集合RMSD、Ramachandran分布和冲突评分。违反约束和RMSD都是不准确的衡量标准。核磁共振与晶体结构的比较表明，二级结构同样准确，但晶体结构在环路中通常过于刚性，而核磁共振结构总体上通常过于松散。我们表明，该方法是对现有精度度量的有用补充。作者提出了一种计算核磁共振结构精度的方法，其中主链化学位移的灵活性与使用刚度理论预测的结构灵活性进行了比较。作者验证了他们的方法，并用它来比较核磁共振和x射线结构的准确性。
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. The authors present a method for calculating the accuracy of an NMR structure, where flexibility from backbone chemical shifts is compared to structural flexibility predicted using rigidity theory. The authors validate their method and use it to compare the accuracy of NMR and X-ray structures.
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DOI：
10.1016/j.str.2017.10.009
发表时间：
2017-12-05
期刊：
Structure (London, England : 1993)
影响因子：
--
作者：
Gore S;Sanz García E;Hendrickx PMS;Gutmanas A;Westbrook JD;Yang H;Feng Z;Baskaran K;Berrisford JM;Hudson BP;Ikegawa Y;Kobayashi N;Lawson CL;Mading S;Mak L;Mukhopadhyay A;Oldfield TJ;Patwardhan A;Peisach E;Sahni G;Sekharan MR;Sen S;Shao C;Smart OS;Ulrich EL;Yamashita R;Quesada M;Young JY;Nakamura H;Markley JL;Berman HM;Burley SK;Velankar S;Kleywegt GJ
通讯作者：
Kleywegt GJ
影响因子：
2.7
作者：
Berjanskii, Mark V.;Wishart, David S.
通讯作者：
Wishart, David S.
影响因子：
56.9
作者：
BRUNGER, AT;CLORE, GM;NILGES, M
通讯作者：
NILGES, M
影响因子：
2.9
作者：
Keedy, Daniel A.;Williams, Christopher J.;Richardson, Jane S.
通讯作者：
Richardson, Jane S.
DOI：
10.1107/s0907444998003254
发表时间：
1998-09-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Brunger, AT;Adams, PD;Warren, GL
通讯作者：
Warren, GL