DPP-PseAAC: A DNA-binding protein prediction model using Chou's general PseAAC

Journal of Theoretical Biology
M Saifur RahmanM Sohel Rahman

Abstract

A DNA-binding protein (DNA-BP) is a protein that can bind and interact with a DNA. Identification of DNA-BPs using experimental methods is expensive as well as time consuming. As such, fast and accurate computational methods are sought for predicting whether a protein can bind with a DNA or not. In this paper, we focus on building a new computational model to identify DNA-BPs in an efficient and accurate way. Our model extracts meaningful information directly from the protein sequences, without any dependence on functional domain or structural information. After feature extraction, we have employed Random Forest (RF) model to rank the features. Afterwards, we have used Recursive Feature Elimination (RFE) method to extract an optimal set of features and trained a prediction model using Support Vector Machine (SVM) with linear kernel. Our proposed method, named as DNA-binding Protein Prediction model using Chou's general PseAAC (DPP-PseAAC), demonstrates superior performance compared to the state-of-the-art predictors on standard benchmark dataset. DPP-PseAAC achieves accuracy values of 93.21%, 95.91% and 77.42% for 10-fold cross-validation test, jackknife test and independent test respectively. The source code of DPP-PseAAC, alo...Continue Reading

Citations

Jan 3, 2020·Molecular Genetics and Genomics : MGG·Kuo-Chen Chou
Apr 18, 2020·Computational and Mathematical Methods in Medicine·Xiuzhi SangTaigang Liu
Apr 16, 2020·Frontiers in Microbiology·María Lamprecht-GrandíoJosé Eduardo González-Pastor
Sep 7, 2018·Molecular Genetics and Genomics : MGG·Md Siddiqur RahmanSwakkhar Shatabda
Jul 22, 2020·BMC Bioinformatics·Wei WangYuan Zhao
May 1, 2021·Computational Biology and Chemistry·Samia Tasnim SaraSwakkhar Shatabda
May 2, 2021·Computational Biology and Chemistry·H M Fazlul HaqueSwakkhar Shatabda
May 8, 2021·Computational Biology and Chemistry·Sayed Mehedi AzimSwakkhar Shatabda
Jun 2, 2021·BMC Bioinformatics·Yuqing QianFei Guo
Jan 8, 2021·Journal of Chemical Information and Modeling·Jun HuDong-Jun Yu
Aug 21, 2021·Bioinformatics·Alexander ZaitzeffJedediah M Singer

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