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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors.

ABSTRACT: We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can be extended to epigenetic variants, mismatches, mutations, or any non-coding nucleobases. When complemented with chromatin structure information, our in vitro trained method provides also good estimates of in vivo binding sites in yeast.

SUBMITTER: Barissi S

PROVIDER: S-EPMC9458447 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors.

Barissi Sandro S Sala Alba A Wieczór Miłosz M Battistini Federica F Orozco Modesto M

Nucleic acids research 20220901 16

We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can be extended to epigenetic variants, mismatches, mutations, or any n ...[more]

PMID: 36018808

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