Department of Chemical and Biological Engineering, Koc University, 34450 Istanbul, Turkey; Center for Computational Biology and Bioinformatics, Koc University, 34450 Istanbul, Turkey.
Department of Computer Engineering, Koc University, 34450 Istanbul, Turkey; Center for Computational Biology and Bioinformatics, Koc University, 34450 Istanbul, Turkey.
Curr Opin Struct Biol. 2015 Dec;35:87-92. doi: 10.1016/j.sbi.2015.10.001. Epub 2015 Nov 9.
The increase in the number of structurally determined protein complexes strengthens template-based docking (TBD) methods for modelling protein-protein interactions (PPIs). These methods utilize the known structures of protein complexes as templates to predict the quaternary structure of the target proteins. The templates may be partial or complete structures. Interface based (partial) methods have recently gained interest due in part to the observation that the interface regions are reusable. We describe how available template interfaces can be used to obtain the structural models of protein interactions. Despite the agreement that a majority of the protein complexes can be modelled using the available Protein Data Bank (PDB) structures, a handful of studies argue that we need more template proteins to increase the structural coverage of PPIs. We also discuss the performance of the interface TBD methods at large scale, and the significance of capturing multiple conformations for improving accuracy.
结构确定的蛋白质复合物数量的增加，加强了基于模板的对接（TBD）方法在蛋白质-蛋白质相互作用（PPIs）建模中的应用。这些方法利用已知的蛋白质复合物结构作为模板，来预测目标蛋白质的四级结构。模板可以是部分的或完整的结构。基于界面（部分）的方法最近引起了人们的兴趣，部分原因是观察到界面区域是可重复使用的。我们描述了如何利用可用的模板界面来获得蛋白质相互作用的结构模型。尽管大多数蛋白质复合物可以使用现有的蛋白质数据库（PDB）结构进行建模已经达成共识，但少数研究认为，我们需要更多的模板蛋白质来增加 PPIs 的结构覆盖率。我们还讨论了界面 TBD 方法在大规模上的性能，以及捕获多种构象以提高准确性的重要性。
