Miniprotein Design

This repository contains computational tools and data for miniprotein design targeting BRD3 ET domain

Repository Structure

input_pdbs/

Structures of motifs bound to ET domains used as initial templates.

design_scripts/

• rf_motif.slurm: RFDiffusion backbone generation
• mpnn.slurm: ProteinMPNN-FastRelax and AF2 initial guess

sequences/

Collection of sequences organized based on results from AI-based filtering

• seqs_positive.dat: Sequences that successfully passed all filters
• seqs_negative.dat: Sequences that failed in at least one of the filters
• seqs_random.dat: Reference set of 5 random miniproteins used for AF-CBA

meld_summary/

AlphaFold2 and MELD structures (centroid of top clusters) of both the ET-miniprotein complexes and miniprotein monomers

• meld_summary.pdf: summary of results from the different filtering stages