Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.
Department of Computer Science, Purdue University, West Lafayette, Indiana, USA.
Proteins. 2022 Jan;90(1):83-95. doi: 10.1002/prot.26188. Epub 2021 Aug 3.
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.
蛋白质结构对接是指根据蛋白质亚基的个别三级结构预测蛋白质复合物的四级结构的过程。蛋白质对接通常分为两个主要步骤。首先将亚基对接，同时保持它们的刚性以形成复合物，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应用至关重要，因为它旨在纠正相互作用残基和界面处原子的构象。在这里，我们在蛋白质复合物模型的细化中对 8 种现有的蛋白质结构细化方法的性能进行了基准测试。我们表明，亚基之间的天然接触分数是迄今为止最直接的改进指标。然而，基于均方根偏差的基于骨架的指标在通过细化来改进时则更加困难。
