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首页> 外文期刊>Proteins: Structure, Function, and Genetics >An improved protein decoy set for testing energy functions for protein structure prediction.
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An improved protein decoy set for testing energy functions for protein structure prediction.

机译：一种改进的蛋白质诱饵组，用于测试能量功能以预测蛋白质结构。

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We have improved the original Rosetta centroid/backbone decoy set by increasing the number of proteins and frequency of near native models and by building on sidechains and minimizing clashes. The new set consists of 1,400 model structures for 78 different and diverse protein targets and provides a challenging set for the testing and evaluation of scoring functions. We evaluated the extent to which a variety of all-atom energy functions could identify the native and close-to-native structures in the new decoy sets. Of various implicit solvent models, we found that a solvent-accessible surface area-based solvation provided the best enrichment and discrimination of close-to-native decoys. The combination of this solvation treatment with Lennard Jones terms and the original Rosetta energy provided better enrichment and discrimination than any of the individual terms. The results also highlight the differences in accuracy of NMR and X-ray crystal structures: a large energy gap was observed between native and non-native conformations for X-ray structures but not for NMR structures.
机译：我们通过增加蛋白质数量和接近天然模型的频率，并在侧链上构建并最大程度地减少了冲突，改进了原始的Rosetta质心/骨干诱饵集。新的集合由1,400个模型结构组成，可用于78个不同的蛋白质目标，并为测试和评估评分功能提供了具有挑战性的集合。我们评估了各种全原子能函数可以识别新诱饵组中的自然结构和接近自然结构的程度。在各种隐式溶剂模型中，我们发现基于溶剂可及表面积的溶剂化方法提供了最接近天然诱饵的最佳富集度和判别力。这种溶剂化处理与Lennard Jones术语和原始的Rosetta能量相结合，提供了比任何单个术语更好的富集和区分效果。结果还突出显示了NMR和X射线晶体结构准确性的差异：在X射线结构的天然构象和非天然构象之间观察到较大的能隙，而NMR结构没有观察到。

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