westlake-repl/SaProt

Issues

• Question about the missing weight from the model checkpoint

  #77 opened a month ago by AllanLZhang
  2

• Using Foldseek when there are no PDBs

  #76 opened 2 months ago by Yangqy-16
  2

• An easy issue

  #75 opened 2 months ago by hello257
  4

• What does the key of ''valid mask" means in contact dataset?

  #74 opened 2 months ago by heya5
  2

• 1) sequence recovery (sequence design) code request 2) generating .mdb file 3) PEFT 4) best model selection after training

  #73 opened 2 months ago by sj584
  1

• finetuning with MLM task

  #70 opened 2 months ago by sj584
  5

• How to fine tune locally with SaProtHub datasets?

  #72 opened 2 months ago by dc2211
  11

• LightingModule optimizer issue - Thermostability fine-tuning

  #71 opened 2 months ago by dc2211
  5

• Downloading pretraining dataset from huggingface

  #43 opened 6 months ago by rubenweitzman
  3

• Can I post training SaProt?

  #68 opened 2 months ago by har77774
  12

• Enable checkpointing Error when pretraining

  #69 opened 3 months ago by zz-lovely
  4

• fine-tuning with more protein sequences

  #53 opened 5 months ago by avilella
  10

• code for pretraining

  #67 opened 3 months ago by done520
  1

• Key error when using aa sequence

  #66 opened 3 months ago by HelloWorldLTY
  2

• Interpretation of predicted mutation effect

  #64 opened 3 months ago by TangYiChing
  1

• Embedding generation

  #65 opened 3 months ago by idmjky
  0

• ERROR: No matching distribution found for pytorch-lightning==1.8.3

  #62 opened 3 months ago by TangYiChing
  1

• Training SaProt with a smaller ESM model

  #45 opened 6 months ago by BSharmi
  3

• Mutation location

  #63 opened 3 months ago by TangYiChing
  4

• PDB Validation set for figure 2

  #61 opened 4 months ago by alex-hh
  1

• how to extract embeddings of the SaProt model

  #49 opened 6 months ago by wangjiaqi8710
  1

• Dimension error

  #60 opened 4 months ago by 1412140736
  0

• KeyError: 'XcXgXyXtXyXgXd

  #59 opened 4 months ago by 1412140736
  1

• Multiple mutation prediction

  #58 opened 4 months ago by wangjs188
  4

• the results of DMS fitness in the ProteinGym benchmark

  #57 opened 5 months ago by jiaolifengmi
  1

• What is the config_path in "Predict mutational effect" part?

  #56 opened 5 months ago by LAJ-THU
  2

• Fine-tune SaProt on the Thermostability task

  #38 opened 7 months ago by qiyifei1
  4

• Temperature (pLDDT) masking for multiple chain PDB files

  #55 opened 5 months ago by Hrovatin
  4

• Model use - relative imports

  #54 opened 5 months ago by Hrovatin
  4

• How to use SaProt as an encoder just like esm

  #52 opened 5 months ago by KyrieYsPKU
  1

• Is there a way to test/compute high load mutational effects on some datasets?

  #51 opened 5 months ago by Yang-Wang-2020
  4

• Inconsistency in number of classes in EC/GO downstream datasets

  #50 opened 5 months ago by klemens-floege
  1

• Contact map prediction

  #48 opened 6 months ago by gezmi
  1

• can not use foldseek

  #47 opened 6 months ago by WenxiangL
  1

• Evaluate multiple mutation effect

  #46 opened 6 months ago by dc2211
  5

• How to interpret mutational effect output?

  #44 opened 6 months ago by dc2211
  2

• How to download cif files?

  #41 opened 6 months ago by Guardian-in-the-WF
  1

• Output dimension

  #42 opened 6 months ago by douzhuang
  1

• Dataset overlap

  #40 opened 7 months ago by lhallee
  2

• Guideline for fine-tuning a pre-trained model with specific protein thermal stability data

  #39 opened 7 months ago by biowander
  2

• Inconsistent config in `SaProt_35M_AF2.pt` when loading by the esm implementation

  #37 opened 7 months ago by chAwater
  1

• How can I use Saprot to predict the mutational effects on my own protein?

  #36 opened 7 months ago by AaranWang
  9

• How / where do I tell SaProt to use the fine tuned model?

  #35 opened 7 months ago by nogako
  4

• Reproducibility issues - Different scores than the ones from ProteinGym

  #33 opened 7 months ago by geduran
  7

• How to reproduce the SaProt_35M_AF2?

  #34 opened 7 months ago by AaranWang
  9

• How to use my own dataset

  #32 opened 7 months ago by Colin-Jay
  5

• Problem of 'Some weights of EsmForMaskedLM were not initialized from the model checkpoint at ./SaProt_model and are newly initialized'

  #30 opened 8 months ago by Gryff1ndor
  1

• 'utf-8' codec can't decode byte 0x80 in position 64: invalid start byte

  #31 opened 8 months ago by tmai-juv
  1

• per residue representations

  #28 opened 8 months ago by FlorianWieser1
  2

• Mismatch between ESM2 pretraining dataset and SaProt pretraining dataset

  #27 opened 9 months ago by ItamarChinn
  1