dauparas/ProteinMPNN

Issues

• training with a custom dataset

  #54 opened a year ago by adrienchaton
  5

• No chain_set_test.jsonl file in the root directory

  #111 opened 2 months ago by Eager-to-earn-money-standing-up
  0

• How to confirm the global polar amino acid bias value? What is the meaning of 1.39?

  #110 opened 2 months ago by luojc712
  0

• --omit_AA "CM" parameter?

  #109 opened 2 months ago by Jahyunhong
  0

• jsonl file to pdb

  #108 opened 2 months ago by ahorvath
  0

• What is the difference between --conditional_probs_only_backbone and --unconditional_probs_only

  #97 opened 5 months ago by tsjain
  1

• `parse_cif_noX.py` misses some chains in CATH?

  #82 opened 9 months ago by tyang816
  2

• what pdbx package does parse_cif_noX.py expect?

  #105 opened 4 months ago by cseed
  1

• No use of GPU?

  #107 opened 3 months ago by khayatlab
  0

• Global_score

  #106 opened 4 months ago by zjlclimb
  0

• Sampling temperature for flexible chains

  #104 opened 4 months ago by Davood-Norouzi
  0

• .Fa Output reorganization question

  #103 opened 4 months ago by noah-c-noah-do
  0

• Questions about model weights

  #100 opened 5 months ago by mh8859
  0

• RuntimeError: Class values must be smaller than num_classes. | protein_mpnn_utils.py & mask_size issue?

  #99 opened 5 months ago by emilyrkang
  0

• Empty parsed_pdbs.jsonl file from parse_multiple_chains.py helper script?

  #98 opened 5 months ago by emilyrkang
  1

• Training time

  #96 opened 6 months ago by sahamitul
  1

• Creates hydrophobic surface patches wit many Ala side chains

  #95 opened 6 months ago by gha2012
  2

• Error in running colab version.

  #58 opened a year ago by SnehaBheemireddy
  0

• Where is the LigandMPNN

  #72 opened a year ago by chengyunzhang
  2

• Model is adding an amino acid to the original sequence

  #92 opened 6 months ago by tony-res
  5

• Amino acid sequence has too many "K/E"

  #89 opened 7 months ago by kjogr12
  2

• Need of assistance and advising

  #91 opened 6 months ago by Hanoriega
  0

• Clarify 'design chains'

  #78 opened 9 months ago by jadolfbr
  1

• How do I use a PSSM with proteinMPNN?

  #90 opened 7 months ago by proteins247
  0

• Design complexes with unknown chains (proposed fix included)

  #86 opened 7 months ago by SimonCrouzet
  0

• whether to redesign low confidence aas

  #85 opened 8 months ago by 18217265596
  0

• Retrieve per-position scores or score a chain in the context of another

  #84 opened 8 months ago by amin-sagar
  0

• Warnings From Example Scripts?

  #81 opened 8 months ago by jamesrgraham
  2

• Training model

  #83 opened 8 months ago by luoyu5023
  0

• conditional_probs_only_backbone is ignored when used alone

  #80 opened 9 months ago by TCoulth
  0

• Indexing with Missing Residues

  #77 opened 10 months ago by brucejwittmann
  4

• Designing Interface Residues

  #62 opened a year ago by linamp
  1

• Tying Multiple Chains Independently

  #76 opened 10 months ago by brucejwittmann
  4

• From 2 distinct structure to a single sequence ?

  #75 opened 10 months ago by PodevynLoris
  4

• Question about global vs local score

  #74 opened 10 months ago by jadolfbr
  1

• --bias_by_res_jsonl example?

  #73 opened 10 months ago by tony-res
  3

• What constitutes a "low quality" backbone?

  #61 opened a year ago by bwllc
  4

• question: prob vs log_prob matrices

  #71 opened a year ago by agarrubio
  0

• mmseq clustering logic

  #52 opened a year ago by OliviaViessmann
  2

• limit to number of chains in homooligomers

  #69 opened a year ago by acarbn
  1

• Usage of --omit_AA_jsonl

  #68 opened a year ago by Cookiemaster33
  0

• Omit AAs per resiude

  #65 opened a year ago by Cookiemaster33
  2

• Is there a way to set a maximum number of mutations per designed sequence?

  #64 opened a year ago by noah-c-noah-do
  2

• What's the numbering scheme for fixed_residues?

  #63 opened a year ago by tony-res
  0

• How to prepare input files for fine-tuning with multimers?

  #60 opened a year ago by gezmi
  0

• Choosing the redesigned structure

  #59 opened a year ago by barthelemymp
  0

• Using multiple input structures for a single sequence output

  #57 opened a year ago by acarbn
  2

• question about dataset

  #53 opened a year ago by MaoSihong
  0

• Safety of generated sequences

  #50 opened a year ago by remybonnav
  1

• Disallow --use_soluble_model if --ca_only is specified

  #51 opened a year ago by jacobastern
  1