westlake-repl SaProt issues

westlake-repl / SaProt

Saprot: Protein Language Model with Structural Alphabet (AA+3Di)

MIT License

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issues

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Question about the missing weight from the model checkpoint

#77 AllanLZhang closed 1 day ago
2
Using Foldseek when there are no PDBs

#76 Yangqy-16 closed 3 days ago
2
An easy issue

#75 hello257 closed 5 days ago
4
What does the key of ''valid mask" means in contact dataset?

#74 heya5 closed 5 days ago
2
1) sequence recovery (sequence design) code request 2) generating .mdb file 3) PEFT 4) best model selection after training

#73 sj584 opened 1 week ago
1
How to fine tune locally with SaProtHub datasets?

#72 dc2211 opened 2 weeks ago
11
LightingModule optimizer issue - Thermostability fine-tuning

#71 dc2211 opened 2 weeks ago
5
finetuning with MLM task

#70 sj584 opened 4 weeks ago
5
Enable checkpointing Error when pretraining

#69 zz-lovely closed 1 month ago
4
Can I post training SaProt?

#68 har77774 closed 1 month ago
12
code for pretraining

#67 done520 opened 1 month ago
1
Key error when using aa sequence

#66 HelloWorldLTY closed 1 month ago
2
Embedding generation

#65 idmjky closed 2 months ago
0
Interpretation of predicted mutation effect

#64 TangYiChing opened 2 months ago
1
Mutation location

#63 TangYiChing closed 2 months ago
4
ERROR: No matching distribution found for pytorch-lightning==1.8.3

#62 TangYiChing closed 2 months ago
1
PDB Validation set for figure 2

#61 alex-hh opened 2 months ago
1
Dimension error

#60 1412140736 closed 2 months ago
0
KeyError: 'XcXgXyXtXyXgXd

#59 1412140736 opened 2 months ago
1
Multiple mutation prediction

#58 wangjs188 closed 3 months ago
4
the results of DMS fitness in the ProteinGym benchmark

#57 jiaolifengmi opened 3 months ago
1
What is the config_path in "Predict mutational effect" part?

#56 LAJ-THU closed 3 months ago
2
Temperature (pLDDT) masking for multiple chain PDB files

#55 Hrovatin opened 3 months ago
4
Model use - relative imports

#54 Hrovatin opened 3 months ago
4
fine-tuning with more protein sequences

#53 avilella opened 3 months ago
10
How to use SaProt as an encoder just like esm

#52 KyrieYsPKU opened 3 months ago
1
Is there a way to test/compute high load mutational effects on some datasets?

#51 Yang-Wang-2020 closed 3 months ago
4
Inconsistency in number of classes in EC/GO downstream datasets

#50 klemens-floege opened 4 months ago
1
how to extract embeddings of the SaProt model

#49 wangjiaqi8710 closed 4 months ago
1
Contact map prediction

#48 gezmi opened 4 months ago
1
can not use foldseek

#47 WenxiangL opened 4 months ago
1
Evaluate multiple mutation effect

#46 dc2211 closed 4 months ago
5
Training SaProt with a smaller ESM model

#45 BSharmi opened 4 months ago
3
How to interpret mutational effect output?

#44 dc2211 closed 4 months ago
2
Downloading pretraining dataset from huggingface

#43 rubenweitzman opened 4 months ago
3
Output dimension

#42 douzhuang closed 5 months ago
1
How to download cif files?

#41 Guardian-in-the-WF closed 4 months ago
1
Dataset overlap

#40 lhallee closed 5 months ago
2
Guideline for fine-tuning a pre-trained model with specific protein thermal stability data

#39 biowander closed 5 months ago
2
Fine-tune SaProt on the Thermostability task

#38 qiyifei1 closed 5 months ago
4
Inconsistent config in `SaProt_35M_AF2.pt` when loading by the esm implementation

#37 chAwater closed 5 months ago
1
How can I use Saprot to predict the mutational effects on my own protein?

#36 AaranWang closed 5 months ago
9
How / where do I tell SaProt to use the fine tuned model?

#35 nogako closed 5 months ago
4
How to reproduce the SaProt_35M_AF2?

#34 AaranWang closed 5 months ago
9
Reproducibility issues - Different scores than the ones from ProteinGym

#33 geduran closed 5 months ago
7
How to use my own dataset

#32 Colin-Jay closed 6 months ago
5
'utf-8' codec can't decode byte 0x80 in position 64: invalid start byte

#31 tmai-juv closed 6 months ago
1
Problem of 'Some weights of EsmForMaskedLM were not initialized from the model checkpoint at ./SaProt_model and are newly initialized'

#30 Gryff1ndor closed 6 months ago
1
Add missing import

#29 memgonzales closed 7 months ago
1
per residue representations

#28 FlorianWieser1 closed 7 months ago
2