StackDPPred: a stacking based prediction of DNA-binding protein from sequence

Bioinformatics
Avdesh MishraMd Tamjidul Hoque

Abstract

Identification of DNA-binding proteins from only sequence information is one of the most challenging problems in the field of genome annotation. DNA-binding proteins play an important role in various biological processes such as DNA replication, repair, transcription and splicing. Existing experimental techniques for identifying DNA-binding proteins are time-consuming and expensive. Thus, prediction of DNA-binding proteins from sequences alone using computational methods can be useful to quickly annotate and guide the experimental process. Most of the methods developed for predicting DNA-binding proteins use the information from the evolutionary profile, called the position-specific scoring matrix (PSSM) profile, alone and the accuracies of such methods have been limited. Here, we propose a method, called StackDPPred, which utilizes features extracted from PSSM and residue specific contact-energy to help train a stacking based machine learning method for the effective prediction of DNA-binding proteins. Based on benchmark sequences of 1063 (518 DNA-binding and 545 non DNA-binding) proteins and using jackknife validation, StackDPPred achieved an ACC of 89.96%, MCC of 0.799 and AUC of 94.50%. This outcome outperforms several stat...Continue Reading

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Citations

Aug 24, 2018·International Journal of Molecular Sciences·Yumeng LiuBin Liu
Apr 9, 2019·Briefings in Bioinformatics·Sijia ZhangJunfeng Xia
Apr 18, 2020·Computational and Mathematical Methods in Medicine·Xiuzhi SangTaigang Liu
Feb 8, 2021·Computational Biology and Chemistry·Avdesh MishraMd Tamjidul Hoque
Mar 10, 2021·Artificial Intelligence in Medicine·Avdesh MishraTamjidul Hoque
Jul 7, 2021·Briefings in Bioinformatics·Fuyi LiLachlan J M Coin
Aug 21, 2021·Briefings in Bioinformatics·Jian ZhangLukasz Kurgan
Aug 21, 2021·Bioinformatics·Alexander ZaitzeffJedediah M Singer
Nov 4, 2021·Interdisciplinary Sciences, Computational Life Sciences·Yan ZhangBin Yu

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