Comments (4)
LiorZ
commented on August 19, 2024
AFAIK from reading the soluble analogues of integral membrane protein before using the soluble version of protein-mpnn they used AF2seq (https://github.com/bene837/af2seq) to generate the topologies.
Have you tried that before running MPNN?
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amin-sagar
commented on August 19, 2024
I have had a similar experience. It would be great to know what sampling temperature was used in the original paper.
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dauparas
commented on August 19, 2024
We have updated solubleMPNN model weights. Try using the latest version and let us know if there are still hydrophobic AAs on the surface.
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SkwisgaarSkwigelf
commented on August 19, 2024
Thank you, I tried with the new weights (along with using AF2seq to change the starting sequence of my input) and my outputs now appear much more soluble (fewer surface hydrophobics and better scores than manually biasing against hydrophobics).
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Related Issues (20)
- Questions about model weights
- .Fa Output reorganization question
- Sampling temperature for flexible chains
- what pdbx package does parse_cif_noX.py expect? HOT 2
- Global_score
- No use of GPU?
- jsonl file to pdb
- --omit_AA "CM" parameter?
- How to confirm the global polar amino acid bias value? What is the meaning of 1.39?
- No chain_set_test.jsonl file in the root directory
- Design complexes with unknown chains (proposed fix included)
- Amino acid sequence has too many "K/E" HOT 2
- How do I use a PSSM with proteinMPNN?
- Need of assistance and advising
- Model is adding an amino acid to the original sequence HOT 5
- Creates hydrophobic surface patches wit many Ala side chains HOT 2
- Training time HOT 1
- What is the difference between --conditional_probs_only_backbone and --unconditional_probs_only HOT 1
- Empty parsed_pdbs.jsonl file from parse_multiple_chains.py helper script? HOT 1
- RuntimeError: Class values must be smaller than num_classes. | protein_mpnn_utils.py & mask_size issue?
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