Computational learning on specificity-determining residue-nucleotide interactions
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ArticleDate
2015-11-02Permanent link to this record
http://hdl.handle.net/10754/592815
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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.Citation
Computational learning on specificity-determining residue-nucleotide interactions 2015:gkv1134 Nucleic Acids ResearchPublisher
Oxford University Press (OUP)Journal
Nucleic Acids ResearchPubMed ID
26527718Additional Links
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1134ae974a485f413a2113503eed53cd6c53
10.1093/nar/gkv1134