rosettacommons/ligandmpnn repository overview

⁠Official LigandMPNN image maintained by rosettacommons.org⁠

This image is built from the LigandMPNN repository that provides inference code for both ProteinMPNN and LigandMPNN.

LigandMPNN is fully open-source under an MIT License whose full text can be found here⁠.

Please note that this image is not compatible with systems using the ARM architecture.

⁠Example syntax

⁠Using Docker

docker run -it --rm \
-v /path/to/your/input_dir:/input \
-v /path/to/your/output_dir:/output \
rosettacommons/ligandmpnn \ 
--model_type 'protein_mpnn' \
--pdb_path /input/1BC8.pdb \
--out_folder /output

⁠Using Apptainer (or Singularity)

The instructions below use Apptainer, but the same commands will work with Singularity.

To run the image using Apptainer you need to pull it using

apptainer pull ligandmpnn.sif docker://rosettacommons/ligandmpnn

Then you can use it very similarly to the Docker example above:

apptainer run --nv \
ligandmpnn.sif \
--model_type 'protein_mpnn' \
--pdb_path /path/to/your/input_dir/1BC8.pdb \
--out_folder /path/to/your/output_dir/"
--checkpoint_protein_mpnn '/app/ligandmpnn/model_params/proteinmpnn_v_48_020.pt'

You will need to change the checkpoint_protein_mpnn path and option name depending on the model weights you want to use

Please contact us with any questions, feedback, or issues you have concerning these containers here⁠.