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Benchmarking of structure refinement methods for protein complex models
Proteins: Structure, Function, and Bioinformatics ( IF 2.9 ) Pub Date : 2021-07-26 , DOI: 10.1002/prot.26188
Jacob Verburgt 1 , Daisuke Kihara 1, 2, 3
Affiliation  

Protein structure docking is the process in which the quaternary structure of a protein complex is predicted from individual tertiary structures of the protein subunits. Protein docking is typically performed in two main steps. The subunits are first docked while keeping them rigid to form the complex, which is then followed by structure refinement. Structure refinement is crucial for a practical use of computational protein docking models, as it is aimed for correcting conformations of interacting residues and atoms at the interface. Here, we benchmarked the performance of eight existing protein structure refinement methods in refinement of protein complex models. We show that the fraction of native contacts between subunits is by far the most straightforward metric to improve. However, backbone dependent metrics, based on the Root Mean Square Deviation proved more difficult to improve via refinement.

中文翻译:

蛋白质复杂模型结构细化方法的基准测试

蛋白质结构对接是从蛋白质亚基的各个三级结构预测蛋白质复合物的四级结构的过程。蛋白质对接通常分两个主要步骤进行。首先对接亚基,同时保持它们的刚性以形成复合体,然后进行结构细化。结构细化对于计算蛋白质对接模型的实际使用至关重要,因为它旨在纠正界面处相互作用的残基和原子的构象。在这里,我们对八种现有蛋白质结构改进方法在改进蛋白质复杂模型中的性能进行了基准测试。我们表明,亚基之间的原生接触比例是迄今为止最直接的改进指标。然而,骨干相关指标,
更新日期:2021-07-26
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