title: An overview of the prediction of protein DNA-binding sites.
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 prediction methods, increased performance, or practical applications.
authors.affiliation: Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. jingnasi@bjfu.edu.cn.
authors.forename: Jingna
authors.initials: J
authors.lastname: Si
authors.affiliation: Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. ruizhao@bjfu.edu.cn.
authors.forename: Rui
authors.initials: R
authors.lastname: Zhao
authors.affiliation: Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. RWu@bjfu.edu.cn.
authors.forename: Rongling
authors.initials: R
authors.lastname: Wu
mesh_terms: D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D001665:Binding Sites; D019295:Computational Biology; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D011485:Protein Binding
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA