A Novel Network-based Computational Model for Prediction of Essential Proteins

• Published in: IEEE access Vol. 8; p. 1
• Main Authors: Zhu, Xianyou, Liu, Yang, Pei, Tingrui, Chen, Zhiping, Li, Xueyong, Wang, Lei
• Format: Journal Article
• Language: English
• Published: Piscataway IEEE 01.01.2020; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Algorithms; Biological system modeling; Computational modeling; Computer networks; Essential protein; PageRank algorithm; Performance evaluation; PPI; Prediction algorithms; Prediction models; Predictive models; Proteins; Search engines; Similarity; SimRank algorithm; Topology
• ISSN: 2169-3536; 2169-3536
• DOI: 10.1109/ACCESS.2020.3012682

Identification of essential proteins is important for understanding cell survival and development, because even if only one of these proteins is missing, organisms cannot survive or develop. Since traditional methods for identifying essential proteins based on biological experiments are costly and inefficient, more and more computational models are proposed for predicting essential proteins in recent years. In this paper, a novel computational model called BSPM is proposed, in which, an original PPI network will be built based on known protein-protein associations first, and then topology information of the original PPI network will be adopted to measure the similarities between proteins based on the SimRank algorithm. Thereafter, a weighted PPI network can be obtained based on the similarities between proteins and the original PPI network. Finally, based on the weighted PPI network, the PageRank algorithm will be used to infer potential essential proteins. Moreover, in order to evaluate the performance of BSPM, we have compared the performance of BSPM with 14 classical prediction models in the field based on two different databases, and experimental results show that BSPM can achieve prediction accuracies of 92%, 81% and 76% out of the top 100, 200 and 300 candidate proteins separately, which not only are significantly better than those 14 competitive classical prediction models, but also means that BSPM can be used as an effective model for identifying essential proteins in the future.