dauparas ProteinMPNN issues

dauparas / ProteinMPNN

Code for the ProteinMPNN paper

MIT License

874 stars 263 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

jsonl file to pdb

#108 ahorvath opened 2 days ago
0
No use of GPU?

#107 khayatlab opened 1 month ago
0
Global_score

#106 zjlclimb opened 2 months ago
0
what pdbx package does parse_cif_noX.py expect?

#105 cseed opened 2 months ago
1
Sampling temperature for flexible chains

#104 Davood-Norouzi opened 2 months ago
0
.Fa Output reorganization question

#103 noah-c-noah-do opened 2 months ago
0
Added a change to LJ-branch to start a new pull request. (Take 2)

#102 laurjones closed 2 months ago
0
Pull Request .01

#101 laurjones closed 2 months ago
0
Questions about model weights

#100 mh8859 opened 2 months ago
0
RuntimeError: Class values must be smaller than num_classes. | protein_mpnn_utils.py & mask_size issue?

#99 emilyrkang opened 3 months ago
0
Empty parsed_pdbs.jsonl file from parse_multiple_chains.py helper script?

#98 emilyrkang closed 3 months ago
1
What is the difference between --conditional_probs_only_backbone and --unconditional_probs_only

#97 tsjain opened 3 months ago
1
Training time

#96 sahamitul opened 4 months ago
1
Creates hydrophobic surface patches wit many Ala side chains

#95 gha2012 opened 4 months ago
2
Fix for issue #92 - Adding proline

#94 tony-res opened 4 months ago
0
Drone

#93 decarboxy closed 4 months ago
0
Model is adding an amino acid to the original sequence

#92 tony-res opened 4 months ago
5
Need of assistance and advising

#91 Hanoriega opened 4 months ago
0
How do I use a PSSM with proteinMPNN?

#90 proteins247 opened 5 months ago
0
Amino acid sequence has too many "K/E"

#89 kjogr12 opened 5 months ago
2
Make the path handling more platform agnostic.

#88 netogallo opened 5 months ago
0
Fix bug related to np.pad() when handling complexes with unknown chains

#87 SimonCrouzet opened 5 months ago
0
Design complexes with unknown chains (proposed fix included)

#86 SimonCrouzet opened 5 months ago
0
whether to redesign low confidence aas

#85 18217265596 opened 5 months ago
0
Retrieve per-position scores or score a chain in the context of another

#84 amin-sagar opened 5 months ago
0
Training model

#83 luoyu5023 opened 6 months ago
0
`parse_cif_noX.py` misses some chains in CATH?

#82 tyang816 opened 7 months ago
2
Warnings From Example Scripts?

#81 jamesrgraham closed 6 months ago
2
conditional_probs_only_backbone is ignored when used alone

#80 TCoulth opened 7 months ago
0
Add error alerts for folder_with_pdbs .pdb error

#79 jfreeze95 opened 7 months ago
0
Clarify 'design chains'

#78 jadolfbr opened 7 months ago
1
Indexing with Missing Residues

#77 brucejwittmann opened 8 months ago
4
Tying Multiple Chains Independently

#76 brucejwittmann closed 8 months ago
4
From 2 distinct structure to a single sequence ?

#75 PodevynLoris opened 8 months ago
4
Question about global vs local score

#74 jadolfbr closed 8 months ago
1
--bias_by_res_jsonl example?

#73 tony-res closed 8 months ago
3
Where is the LigandMPNN

#72 chengyunzhang opened 8 months ago
2
question: prob vs log_prob matrices

#71 agarrubio opened 9 months ago
0
feat: refactored and added setup.py for easy install

#70 maxkazman closed 10 months ago
0
limit to number of chains in homooligomers

#69 acarbn opened 10 months ago
1
Usage of --omit_AA_jsonl

#68 Cookiemaster33 closed 10 months ago
0
Adding progress bar for long jobs

#67 tony-res closed 7 months ago
0
[setup] Add a setup.py

#66 edawson opened 10 months ago
0
Omit AAs per resiude

#65 Cookiemaster33 closed 10 months ago
2
Is there a way to set a maximum number of mutations per designed sequence?

#64 noah-c-noah-do closed 10 months ago
2
What's the numbering scheme for fixed_residues?

#63 tony-res closed 10 months ago
0
Designing Interface Residues

#62 linamp opened 11 months ago
1
What constitutes a "low quality" backbone?

#61 bwllc opened 11 months ago
4
How to prepare input files for fine-tuning with multimers?

#60 gezmi opened 11 months ago
0
Choosing the redesigned structure

#59 barthelemymp opened 1 year ago
0