RFD4-Proteina uses machine learning to design new proteins, generating both their amino acid sequences and proposed three-dimensional structures. It can start from scratch or modify an existing structure while keeping selected parts intact. Applications include designing antibodies, enzymes, and proteins that bind to specific targets.

Reference:

• Corley N, Didi K, Kazman MW, Brent RI, et al
  (2026). Biomolecular design through latent reasoning with RFD4-Proteina
  [Preprint].

• RFD4-Proteina Website

• Module Name: rfd4-proteina (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=12g --cpus-per-task=2 --gres=gpu:a100:1

[user@cn3335 ~]$ mkdir -pv /data/$USER/RFD4_TEST
[user@cn3335 ~]$ cd /data/$USER/RFD4_TEST

[user@cn3335 ~]$ module load rfd4-proteina
[+] Loading rfd4-proteina  0.0.3  on cn3335 
[+] Loading apptainer  1.4.5  on cn3335

[user@cn3335 ~]$ rfd4-proteina rfd4-generate \
    inputs=/opt/RFD4-Proteina/data/benchmarks/monomer/monomer-short.cif.zst \
    num_replicates=1 \
    metrics_tags='[design]' \
    out_dir="$PWD/rfd4-test-$SLURM_JOB_ID" \
    compile_lengths=null
Fetching 2 files: 100%|██████████████████████████| 2/2 [00:00<00:00, 605.41it/s]
Download complete:  |  0.00B            
Reconstruction complete: |      |  0.00B /  0.00B            
sizzling... 🔥 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1/1 0:00:16 • 0:00:00 0.00it/s  
[2026-11-03 08:18:12,473][rfproteina.generate][INFO] - [rank: 0]
✓ Generation complete!
Results saved to /data/user/RFD4_TEST/rfd4-test-34594610

[user@cn3335 ~]$ exit
salloc: Relinquishing job allocation 34594610
[user@biowulf]$								     

Create a batch input file, e.g. rfd4-binder.sh:

#!/bin/sh
#SBATCH --job-name=rfd4-binder
#SBATCH --partition=gpu
#SBATCH --gres=gpu:a100:1
#SBATCH --cpus-per-task=2
#SBATCH --mem=16g
#SBATCH --time=02:00:00

module load rfd4-proteina
mkdir -pv /data/$USER/rfd4-binder-${SLURM_JOB_ID}
cd /data/$USER/rfd4-binder-${SLURM_JOB_ID}

curl -fL -o pdl1.cif \
    https://huggingface.co/nvidia/RFD4-Proteina/resolve/a06e2509c7033b010fc43614e9fd840303588502/examples/protein_binder/input.cif || exit 1

rfd4-proteina rfd4-generate \
    inputs="$PWD/pdl1.cif" \
    num_replicates=8 \
    batch_size=1 \
    num_workers=2 \
    metrics_tags='[design]' \
    seed=42 \
    out_dir="$PWD" \
    compile_lengths=null

Submit this job using the Slurm sbatch command.

sbatch rfd4-proteina.sh