EL_PSSM-RT:DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation

Zhou, Jiyun, Lu, Qin, Xu, Ruifeng, He, Yulan and Wang, Hongpeng (2017). EL_PSSM-RT:DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation. BMC Bioinformatics, 18 ,

Abstract

Background: Prediction of DNA-binding residue is important for understanding the protein-DNA recognition mechanism. Many computational methods have been proposed for the prediction, but most of them do not consider the relationships of evolutionary information between residues. Results: In this paper, we first propose a novel residue encoding method, referred to as the Position Specific Score Matrix (PSSM) Relation Transformation (PSSM-RT), to encode residues by utilizing the relationships of evolutionary information between residues. PDNA-62 and PDNA-224 are used to evaluate PSSM-RT and two existing PSSM encoding methods by five-fold cross-validation. Performance evaluations indicate that PSSM-RT is more effective than previous methods. This validates the point that the relationship of evolutionary information between residues is indeed useful in DNA-binding residue prediction. An ensemble learning classifier (EL_PSSM-RT) is also proposed by combining ensemble learning model and PSSM-RT to better handle the imbalance between binding and non-binding residues in datasets. EL_PSSM-RT is evaluated by five-fold cross-validation using PDNA-62 and PDNA-224 as well as two independent datasets TS-72 and TS-61. Performance comparisons with existing predictors on the four datasets demonstrate that EL_PSSM-RT is the best-performing method among all the predicting methods with improvement between 0.02-0.07 for MCC, 4.18-21.47% for ST and 0.013-0.131 for AUC. Furthermore, we analyze the importance of the pair-relationships extracted by PSSM-RT and the results validates the usefulness of PSSM-RT for encoding DNA-binding residues. Conclusions: We propose a novel prediction method for the prediction of DNA-binding residue with the inclusion of relationship of evolutionary information and ensemble learning. Performance evaluation shows that the relationship of evolutionary information between residues is indeed useful in DNA-binding residue prediction and ensemble learning can be used to address the data imbalance issue between binding and non-binding residues. A web service of EL_PSSM-RT ( http://hlt.hitsz.edu.cn:8080/PSSM-RT_SVM/ ) is provided for free access to the biological research community.

Publication DOI: https://doi.org/10.1186/s12859-017-1792-8
Divisions: Engineering & Applied Sciences > Computer science
Engineering & Applied Sciences > Systems analytics research institute (SARI)
Engineering & Applied Sciences > Computer science research group
Additional Information: © The Author(s). 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Uncontrolled Keywords: DNA-binding residue,DNA-protein interaction,Ensemble learning,PSSM,Random forest,Relation transformation,SVM,Structural Biology,Biochemistry,Molecular Biology,Computer Science Applications,Applied Mathematics
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Related URLs: http://www.scop ... tnerID=8YFLogxK (Scopus URL)
Published Date: 2017-08-29
Authors: Zhou, Jiyun
Lu, Qin
Xu, Ruifeng
He, Yulan ( 0000-0003-3948-5845)
Wang, Hongpeng

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