Interpretable protein-DNA interactions captured by structure-sequence optimization.

ABSTRACT: Sequence-specific DNA recognition underlies essential processes in gene regulation, yet methods for simultaneous predictions of genomic DNA recognition sites and their binding affinity remain lacking. Here, we present the Interpretable protein-DNA Energy Associative (IDEA) model, a residue-level, interpretable biophysical model capable of predicting binding sites and affinities of DNA-binding proteins. By fusing structures and sequences of known protein-DNA complexes into an optimized energy model, IDEA enables direct interpretation of physicochemical interactions among individual amino acids and nucleotides. We demonstrate that this energy model can accurately predict DNA recognition sites and their binding strengths across various protein families. Additionally, the IDEA model is integra

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC12270484 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature