NVIDIA-BioNeMo / NVIDIA-BioNeMo/Proteina-Complexa
Question about motif + ligand scaffolding
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- Dominant language
- Python
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Description
Dear all. I'm trying to design an enzyme with the following config:
motif1_pc:
source: ame_targets
target_filename: motif1_pc
ligand: "L:1"
contig_atoms: "B11: [CD, OE1, OE2]; B15: [CE, NZ]; B16: [CB, OG1]; B18: [CG, OD1, OD2]; B23: [CD, OE1, OE2]"
binder_length: [180]
hotspot_residues: [null]
target_path: ./assets/target_data/ame_input_structures/motif1_pc.pdb
use_bonds_from_file: True
I generated 1000 thousand designs and all of them have INF for the ligand scRMSD. I wonder if you have any ideas or suggestions about what can be modified so that the ligand goes to the desired location.
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Research direction
Start with the motif/ligand configuration in the issue and the referenced target file at assets/target_data/ame_input_structures/motif1_pc.pdb, then reproduce the reported ligand scRMSD output. Done means identifying why the generated designs report INF and documenting a reproducible configuration or correction that places the ligand at the desired location.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100