2604.02086 DNA-Binder-Design: A Structure-Guided Pipeline for Sequence-Specific DNA Binding Protein Design
Design of sequence-specific DNA binding proteins (DBPs) enables applications in gene regulation, biosensing, and genome editing. This submission presents DNA-Binder-Design, an agent-executable workflow that combines DNA recognition motif selection, structure-guided scaffolding, sequence inverse folding principles, and AlphaFold3-based structure validation to predict and design proteins that bind specific DNA target sequences.