Identification of DNA–protein Binding Sites through Multi-Scale Local Average Blocks on Sequence Information

• Published in: Molecules Vol. 22; no. 12; p. 2079
• Main Authors: Shen, Cong, Ding, Yijie, Tang, Jijun, Song, Jian, Guo, Fei
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 28.11.2017; MDPI
• Subjects: Binding sites; Deoxyribonucleic acid; DNA; DNA–protein binding sites; ensemble classifier; feature extraction; Proteins; random sub-sampling; sparse representation model; random sub-sampling; ensemble classifier; feature extraction; sparse representation model; DNA–protein binding sites
• ISSN: 1420-3049; 1433-1373; 1420-3049; 1433-1373
• DOI: 10.3390/molecules22122079

DNA–protein interactions appear as pivotal roles in diverse biological procedures and are paramount for cell metabolism, while identifying them with computational means is a kind of prudent scenario in depleting in vitro and in vivo experimental charging. A variety of state-of-the-art investigations have been elucidated to improve the accuracy of the DNA–protein binding sites prediction. Nevertheless, structure-based approaches are limited under the condition without 3D information, and the predictive validity is still refinable. In this essay, we address a kind of competitive method called Multi-scale Local Average Blocks (MLAB) algorithm to solve this issue. Different from structure-based routes, MLAB exploits a strategy that not only extracts local evolutionary information from primary sequences, but also using predicts solvent accessibility. Moreover, the construction about predictors of DNA–protein binding sites wields an ensemble weighted sparse representation model with random under-sampling. To evaluate the performance of MLAB, we conduct comprehensive experiments of DNA–protein binding sites prediction. MLAB gives M C C of 0.392 , 0.315 , 0.439 and 0.245 on PDNA-543, PDNA-41, PDNA-316 and PDNA-52 datasets, respectively. It shows that MLAB gains advantages by comparing with other outstanding methods. M C C for our method is increased by at least 0.053 , 0.015 and 0.064 on PDNA-543, PDNA-41 and PDNA-316 datasets, respectively.