Faculty of Biology, Technion, Israel Institute of Technology, Haifa, 3200003, Israel.
Department of Computer Science, University of Haifa, Mount Carmel, Haifa, 3498838, Israel.
Sci Rep. 2018 May 29;8(1):8192. doi: 10.1038/s41598-018-26497-z.
The protein interface is key to understand protein function, providing a vital insight on how proteins interact with each other and with other molecules. Over the years, many computational methods to compare protein structures were developed, yet evaluating interface similarity remains a very difficult task. Here, we present PatchBag - a geometry based method for efficient comparison of protein surfaces and interfaces. PatchBag is a Bag-Of-Words approach, which represents complex objects as vectors, enabling to search interface similarity in a highly efficient manner. Using a novel framework for evaluating interface similarity, we show that PatchBag performance is comparable to state-of-the-art alignment-based structural comparison methods. The great advantage of PatchBag is that it does not rely on sequence or fold information, thus enabling to detect similarities between interfaces in unrelated proteins. We propose that PatchBag can contribute to reveal novel evolutionary and functional relationships between protein interfaces.
蛋白质界面是理解蛋白质功能的关键，它提供了关于蛋白质之间以及与其他分子相互作用的重要信息。多年来，已经开发出许多用于比较蛋白质结构的计算方法，但评估界面相似性仍然是一项非常困难的任务。在这里，我们提出了 PatchBag - 一种用于有效比较蛋白质表面和界面的基于几何的方法。PatchBag 是一种基于词汇袋的方法，它将复杂对象表示为向量，从而能够以高效的方式搜索界面相似性。我们使用一种新的评估界面相似性的框架，表明 PatchBag 的性能可与基于最新对齐的结构比较方法相媲美。PatchBag 的巨大优势在于它不依赖于序列或折叠信息，因此能够在不相关的蛋白质之间检测到界面的相似性。我们提出，PatchBag 可以帮助揭示蛋白质界面之间新的进化和功能关系。
