Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings.

ABSTRACT: Knowledge of how proteins interact with DNA is essential for understanding gene regulation. Although DNA-binding specificities for thousands of transcription factors (TFs) have been determined, the specific amino acid-base interactions comprising their structural interfaces are largely unknown. This lack of resolution hampers attempts to leverage these data in order to predict specificities for uncharacterized TFs or TFs mutated in disease. Here we introduce recognition code learning via automated mapping of protein-DNA structural interfaces (rCLAMPS), a probabilistic approach that uses DNA-binding specificities for TFs from the same structural family to simultaneously infer both which nucleotide positions are contacted by particular amino acids within the TF as well as a recognition code

SUBMITTER: Wetzel JL 

PROVIDER: S-EPMC9528988 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature