An overview of the prediction of protein DNA-binding sites

International Journal of Molecular Sciences
Jingna SiRongling Wu

Abstract

Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of different tools, and future directions in protein DNA-binding site prediction. In particular, we detail the meta-analysis of protein DNA-binding sites. We also propose specific implications that are likely to result in novel pre...Continue Reading

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Citations

Nov 6, 2015·International Journal of Molecular Sciences·Jingna SiRongling Wu
Dec 13, 2017·Journal of Molecular Recognition : JMR·A KulandaisamyM Michael Gromiha
Oct 11, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Ricardo Corral-CorralGabriel Del Rio
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Oct 16, 2020·Biotechnology and Applied Biochemistry·Deepak YadavRajasri Bhattacharyya
Oct 30, 2020·Nucleic Acids Research·Bi ZhaoLukasz Kurgan
Jun 3, 2021·International Journal of Molecular Sciences·Samuel Godfrey HendrixZhong-Ru Xie
Sep 19, 2020·Analytical Biochemistry·Ronesh SharmaAlok Sharma
Aug 25, 2020·Current Opinion in Structural Biology·Ilya A Vakser
Aug 21, 2021·Briefings in Bioinformatics·Jian ZhangLukasz Kurgan

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Methods Mentioned

BETA
immunoprecipitation
nuclear magnetic resonance
X-ray
sequence-based
NMR
structure-based predictions

Software Mentioned

PISCES
bnt
metaDBSite
BLAST
blastclust
Delphi
Weka
TFBSshape
PSIPRED
DSSPcont

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