Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA, USA.
Department of Computer Science, Boston University, Boston, MA, USA.
Bioinformatics. 2019 Dec 15;35(24):5374-5378. doi: 10.1093/bioinformatics/btz587.
The complexity of protein-protein interactions (PPIs) is further compounded by the fact that an average protein consists of two or more domains, structurally and evolutionary independent subunits. Experimental studies have demonstrated that an interaction between a pair of proteins is not carried out by all domains constituting each protein, but rather by a select subset. However, determining which domains from each protein mediate the corresponding PPI is a challenging task.
Here, we present domain interaction statistical potential (DISPOT), a simple knowledge-based statistical potential that estimates the propensity of an interaction between a pair of protein domains, given their structural classification of protein (SCOP) family annotations. The statistical potential is derived based on the analysis of >352 000 structurally resolved PPIs obtained from DOMMINO, a comprehensive database of structurally resolved macromolecular interactions.
DISPOT is implemented in Python 2.7 and packaged as an open-source tool. DISPOT is implemented in two modes, basic and auto-extraction. The source code for both modes is available on GitHub: https://github.com/korkinlab/dispot and standalone docker images on DockerHub: https://hub.docker.com/r/korkinlab/dispot. The web server is freely available at http://dispot.korkinlab.org/.
Supplementary data are available at Bioinformatics online.
蛋白质-蛋白质相互作用 (PPIs) 的复杂性进一步加剧，因为平均每个蛋白质由两个或更多的结构和进化上独立的结构域组成。实验研究表明，蛋白质之间的相互作用不是由每个蛋白质的所有结构域进行的，而是由一个选择的子集进行的。然而，确定每个蛋白质中的哪些结构域介导相应的 PPI 是一项具有挑战性的任务。
在这里，我们提出了结构域相互作用统计势能 (DISPOT)，这是一种简单的基于知识的统计势能，用于估计一对蛋白质结构域之间相互作用的倾向，前提是它们的蛋白质结构分类 (SCOP) 家族注释。该统计势能是基于对来自 DOMMINO 的>352000 个结构解析的 PPI 的分析得出的，DOMMINO 是一个结构解析的大分子相互作用的综合数据库。
DISPOT 是用 Python 2.7 编写的，并打包为一个开源工具。DISPOT 有两种模式实现，基本模式和自动提取模式。两种模式的源代码都可以在 GitHub 上获得：https://github.com/korkinlab/dispot 和 DockerHub 上的独立 Docker 映像：https://hub.docker.com/r/korkinlab/dispot。Web 服务器可在 http://dispot.korkinlab.org/ 免费访问。
补充数据可在生物信息学在线获得。
