Miniprotein Design

August 6, 2025 · View on GitHub

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

Pipeline

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