Evaluation of model refinement in CASP13
Evaluation of model refinement in CASP13
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DOI：
10.1002/prot.25794
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发表时间：
2019-08-20
影响因子：
2.9
通讯作者：
Croll, Tristan I.
中科院分区：
文献类型：
--
作者：
Read, Randy J.;Sammito, Massimo D.;Croll, Tristan I.
对第13轮结构预测批判性评估（CASP 13）的模型细化类别的性能进行了评估，结果表明，一些小组持续改进了大多数初始模型，而大多数参与者平均继续降低初始模型。使用为CASP12开发的排名公式，32个组中只有7个组的表现优于仅提交初始模型的“天真预测者”。他们的方法的共同特点包括依赖于基于物理的力场来判断替代构象，以及使用分子动力学将模型放松到局部最小值，通常有一些限制以防止过大的运动。除了传统的CASP指标，主要集中在质量的整体折叠，替代指标进行评估，包括比较的主链和侧链扭转角，和实用的模型解决晶体结构的分子置换法。有人建议，这些指标的引入，以及考虑到坐标误差估计的准确性，将提高良好和非常好的模型之间的歧视。
Performance in the model refinement category of the 13th round of Critical Assessment of Structure Prediction (CASP13) is assessed, showing that some groups consistently improve most starting models whereas the majority of participants continue to degrade the starting model on average. Using the ranking formula developed for CASP12, it is shown that only 7 of 32 groups perform better than a "naive predictor" who just submits the starting model. Common features in their approaches include a dependence on physics-based force fields to judge alternative conformations and the use of molecular dynamics to relax models to local minima, usually with some restraints to prevent excessively large movements. In addition to the traditional CASP metrics that focus largely on the quality of the overall fold, alternative metrics are evaluated, including comparisons of the main-chain and side-chain torsion angles, and the utility of the models for solving crystal structures by the molecular replacement method. It is proposed that the introduction of these metrics, as well as consideration of the accuracy of coordinate error estimates, would improve the discrimination between good and very good models.