Issues

• --seed 0 silently picks a random seed — print or pin the effective seed

  dauparas/ProteinMPNN#154 · Filter by author barlowa124 opened on Sep 24, 2026

• Request for correction: ProteinMPNN manifest draft in OpenSciFlow

  dauparas/ProteinMPNN#151 · Filter by author kkkniengLiu opened on Jul 6, 2026

• ProteinMPNN appears to modify fixed target sequence during peptide design workflow

  dauparas/ProteinMPNN#149 · Filter by author hyejeongchoi-rgb opened on Apr 24, 2026

• Problem: --chain_id_jsonl and --fixed_positions_jsonl not working as expected (both chains designed)

  dauparas/ProteinMPNN#148 · Filter by author jiaanqiang opened on Apr 8, 2026

• the difference between the conditional_probs_only_backbone mode and the unconditional_probs_only mode

  dauparas/ProteinMPNN#147 · Filter by author Zhongyihang11 opened on Mar 18, 2026

• [Documentation] Simpler explanation?

  dauparas/ProteinMPNN#145 · Filter by author rubyFeedback opened on Jan 28, 2026
  1

• homooligomer and different length

  dauparas/ProteinMPNN#144 · Filter by author MrGao1997 opened on Dec 22, 2025

• What should "--num_examples_per_epoch" be set to?

  dauparas/ProteinMPNN#142 · Filter by author kosonocky opened on Dec 3, 2025
  3

• Best Practices for Large-Scale ProteinMPNN → FastRelax Runs: Are Per-Backbone Designs Truly Independent?

  dauparas/ProteinMPNN#141 · Filter by author kimlab-cnu opened on Nov 29, 2025

• Output interpretation

  dauparas/ProteinMPNN#139 · Filter by author Mossy-Frog opened on Nov 7, 2025
  1

• Security audit results

  dauparas/ProteinMPNN#138 · Filter by author TimCraigCGPS opened on Oct 20, 2025
  2

• Possible bug in model initialization (num_decoder_layers)

  dauparas/ProteinMPNN#136 · Filter by author Snail-TI opened on Aug 26, 2025

• Do amino acid types specified in the input backbone PDB file affect the designed result?

  dauparas/ProteinMPNN#135 · Filter by author daniel-dpq opened on Aug 18, 2025

• Fixed positions JSONL only loads last entry

  dauparas/ProteinMPNN#133 · Filter by author ssiddhantsharma opened on Aug 2, 2025

• How does ProteinMPNN select the sampled sequences to report in the output file?

  dauparas/ProteinMPNN#131 · Filter by author Sohini-git opened on Jun 30, 2025

• How process a batch data?

  dauparas/ProteinMPNN#130 · Filter by author code4luck opened on Jun 21, 2025

• Question about list.csv HASH (mentioned in training/README.md)

  dauparas/ProteinMPNN#129 · Filter by author CyvenH opened on May 29, 2025

• temperature

  dauparas/ProteinMPNN#128 · Filter by author 1a2bfdasfdsg opened on Apr 30, 2025
  1

• why generate an empty .jsonl file?

  dauparas/ProteinMPNN#127 · Filter by author RuiWang03 opened on Apr 12, 2025
  2

• How should I generate the fasta if my pdb file names chains as "H, L, C" rather than "A, B, C"?

  dauparas/ProteinMPNN#126 · Filter by author JonasLi-19 opened on Mar 5, 2025

• How to read the output file .npz?

  dauparas/ProteinMPNN#125 · Filter by author Etic2001 opened on Feb 19, 2025

• Why there is no Cb atom type in parse_PDB function?

  dauparas/ProteinMPNN#124 · Filter by author JonasLi-19 opened on Feb 13, 2025
  1

• Difference between log_probs and probs when set save_probs

  dauparas/ProteinMPNN#123 · Filter by author songmingl opened on Feb 8, 2025
  3

• Combine "specify residues to design" and "homooligomer"

  dauparas/ProteinMPNN#122 · Filter by author MiaYang99 opened on Jan 8, 2025
  1

• torch.load with weights_only=False

  dauparas/ProteinMPNN#121 · Filter by author zymxiaozhu opened on Dec 11, 2024