Computational learning on specificity-determining residue-nucleotide interactions.

Citation data:

Nucleic acids research, ISSN: 1362-4962, Vol: 43, Issue: 21, Page: 10180-9

Publication Year:
2015
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Repository URL:
http://hdl.handle.net/10754/592815
PMID:
26527718
DOI:
10.1093/nar/gkv1134
PMCID:
PMC4666365
Author(s):
Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Moses, Alan M.; Zhang, Zhaolei
Publisher(s):
Oxford University Press (OUP)
Tags:
Biochemistry, Genetics and Molecular Biology
article description
The protein-DNA interactions between transcription factors and transcription factor binding sites are essential activities in gene regulation. To decipher the binding codes, it is a long-standing challenge to understand the binding mechanism across different transcription factor DNA binding families. Past computational learning studies usually focus on learning and predicting the DNA binding residues on protein side. Taking into account both sides (protein and DNA), we propose and describe a computational study for learning the specificity-determining residue-nucleotide interactions of different known DNA-binding domain families. The proposed learning models are compared to state-of-the-art models comprehensively, demonstrating its competitive learning performance. In addition, we describe and propose two applications which demonstrate how the learnt models can provide meaningful insights into protein-DNA interactions across different DNA binding families.