Hello authors,
I am working on a peptide-protein binding design project and am using a computational pipeline that involves RFdiffusion (for backbone generation) -> ProteinMPNN (for sequence design) -> AlphaFold2 (for structure prediction and validation).
I have two questions regarding the potential use of LigandMPNN to replace ProteinMPNN in this pipeline:
Replacing ProteinMPNN with LigandMPNN: Since my goal is to design a peptide that binds to a target protein, I understand that LigandMPNN is specifically designed for tasks with ligand context. Is replacing ProteinMPNN with LigandMPNN in this pipeline a recommended approach for generating high-quality protein-ligand sequences?
Error with pack_side_chains feature: I encountered an error when running LigandMPNN with the pack_side_chains feature enabled. I noticed that this is an optional feature. Is it a mandatory feature for generating high-quality designs, or can I skip it and still get reliable sequences for subsequent experimental validation?
Here is the error and the command I used:
Command:
python ../../run.py \
--model_type "ligand_mpnn" \
--pdb_path "./inputs/1BC8.pdb" \
--out_folder "./outputs/ligandmpnn_default"
--batch_size 3 \
--number_of_batches 2 \
--pack_side_chains 1 \
--number_of_packs_per_design 1
Traceback:
Packing side chains...
Traceback (most recent call last):
File "G:\LigandMPNN\run.py", line 990, in <module>
main(args)
File "G:\LigandMPNN\run.py", line 526, in main
sc_dict = pack_side_chains(
^^^^^^^^^^^^^^^^^
File "G:\LigandMPNN\sc_utils.py", line 114, in pack_side_chains
xyz14_noised = feats.frames_and_literature_positions_to_atom14_pos(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "G:\LigandMPNN\openfold\utils\feats.py", line 253, in frames_and_literature_positions_to_atom14_pos
group_mask = nn.functional.one_hot(
^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: one_hot is only applicable to index tensor.
Thank you for your time and assistance!
Hello authors,
I am working on a peptide-protein binding design project and am using a computational pipeline that involves RFdiffusion (for backbone generation) -> ProteinMPNN (for sequence design) -> AlphaFold2 (for structure prediction and validation).
I have two questions regarding the potential use of LigandMPNN to replace ProteinMPNN in this pipeline:
Replacing ProteinMPNN with LigandMPNN: Since my goal is to design a peptide that binds to a target protein, I understand that LigandMPNN is specifically designed for tasks with ligand context. Is replacing ProteinMPNN with LigandMPNN in this pipeline a recommended approach for generating high-quality protein-ligand sequences?
Error with pack_side_chains feature: I encountered an error when running LigandMPNN with the pack_side_chains feature enabled. I noticed that this is an optional feature. Is it a mandatory feature for generating high-quality designs, or can I skip it and still get reliable sequences for subsequent experimental validation?
Here is the error and the command I used:
Command:
Traceback:
Thank you for your time and assistance!