Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, United States of America.
PLoS One. 2012;7(2):e31349. doi: 10.1371/journal.pone.0031349. Epub 2012 Feb 13.
The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures.
越来越多的共结晶蛋白-蛋白复合物的出现为基于模板的蛋白-蛋白对接提供了机会。结构比对技术在远程目标-模板相似性检测中很有用。比对中所涉及结构的大小对于建模的成功与否很重要。本文描述了一项系统的大规模研究，旨在找到基于结构比对的对接应用中最佳的界面定义/大小。结果表明，界面处小于 12 Å 的截止值对应的结构区域不能充分代表界面的结构细节。随着截止值超过 12 Å 的增加，对于更高精度模型，成功率并没有显著增加，而对于较低精度模型，成功率则下降。在我们基于界面比对的对接中，12 Å 的截止值是最优的，对于蛋白质相互作用网络的大规模应用（例如，在整个基因组的范围内）可能是最佳选择。这些结果为对接方法提供了指导，包括对建模结构的高通量应用。
