Computational learning on specificity-determining residue-nucleotide interactions

Ka-Chun Wong, Yue Li, Chengbin Peng, Alan M. Moses, Zhaolei Zhang

Research output: Contribution to journalArticlepeer-review

20 Scopus citations

Abstract

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.
Original languageEnglish (US)
Pages (from-to)gkv1134
JournalNucleic Acids Research
Volume43
Issue number21
DOIs
StatePublished - Nov 2 2015

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