Use Chou's 5-Step Rule to Predict DNA-Binding Proteins with Evolutionary Information.

Weizhong Lu,Haiou Li,Zhengwei Song,Yijie Ding,Yan Cao,Hongjie Wu,Yu Zhang

doi:10.1155/2020/6984045

Abstract

The knowledge of DNA-binding proteins would help to understand the functions of proteins better in cellular biological processes. Research on the prediction of DNA-binding proteins can promote the research of drug proteins and computer acidified drugs. In recent years, methods based on machine learning are usually used to predict proteins. Although great predicted performance can be achieved via current methods, researchers still need to invest more research in terms of the improvement of predicted performance. In this study, the prediction of DNA-binding proteins is studied from the perspective of evolutionary information and the support vector machine method. One machine learning model for predicting DNA-binding proteins based on evolutionary features by using Chou's 5-step rule is put forward. The results show that great predicted performance is obtained on benchmark dataset PDB1075 and independent dataset PDB186, achieving the accuracy of 86.05% and 75.30%, respectively. Thus, the method proposed is comparable to a certain degree, and it may work even better than other methods to some extent.

Highlights

DNA-related life activities are an indispensable part of life activities of biological cells, and it includes detecting the damage of DNA, the replication of DNA, and the transcription and regulation of the gene
The steps of the experiments are as follows: (1) Firstly, building one method model for the prediction of DNA-binding proteins (DbPs) based on evolutionary information by support vector machine (SVM), benchmark dataset PDB1075 and PDB186 are selected as experimental data
The results show that the model with integrated features has better prediction performance

Summary

Introduction

DNA-related life activities are an indispensable part of life activities of biological cells, and it includes detecting the damage of DNA, the replication of DNA, and the transcription and regulation of the gene. They will not occur without the assistance of specific proteins; on the other hand, protein-DNA interaction regulates the activities. The combination of proteins and DNA-chain’s specific or nonspecific is essential. Proteins related to the life activities of DNA and regulate it are known as DNA-binding proteins (DbPs) [1, 2], which are called helical unstable proteins. It is a kind of protein that can bind with DNA to produce complexes. Because of its crucial role in biological activities, the research of DbP recognition is developed

Methods

Results

Conclusion