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Structure-based prediction of protein-protein interaction network in rice

文献类型： 外文期刊

作者： Sun, Fangnan 1 ; Deng, Yaxin 1 ; Ma, Xiaosong 2 ; Liu, Yuan 1 ; Zhao, Lingxia 1 ; Yu, Shunwu 2 ; Zhang, Lida 1 ;

作者机构： 1.Shanghai Jiao Tong Univ, Sch Agr & Biol, Dept Plant Sci, Shanghai 200240, Peoples R China

2.Shanghai Acad Agr Sci, Shanghai Agrobiol Gene Ctr, Shanghai, Peoples R China

关键词： Rice; protein-protein interaction; interactome; protein docking

期刊名称：GENETICS AND MOLECULAR BIOLOGY （ 影响因子：2.1； 五年影响因子：2.2 ）

ISSN： 1415-4757

年卷期： 2024 年 47 卷 1 期

页码：

收录情况： SCI

摘要： Comprehensive protein -protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein -protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice.

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