westlake-repl SaProt issues

westlake-repl / SaProt

Saprot: Protein Language Model with Structural Alphabet

MIT License

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issues

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Output dimension

#42 douzhuang closed 4 days ago
1
How to download cif files?

#41 Guardian-in-the-WF opened 5 days ago
1
Dataset overlap

#40 lhallee closed 1 week ago
2
Guideline for fine-tuning a pre-trained model with specific protein thermal stability data

#39 biowander closed 1 week ago
2
Fine-tune SaProt on the Thermostability task

#38 qiyifei1 closed 2 weeks ago
2
Inconsistent config in `SaProt_35M_AF2.pt` when loading by the esm implementation

#37 chAwater closed 2 weeks ago
1
How can I use Saprot to predict the mutational effects on my own protein?

#36 AaranWang closed 3 weeks ago
9
How / where do I tell SaProt to use the fine tuned model?

#35 nogako closed 3 weeks ago
4
How to reproduce the SaProt_35M_AF2?

#34 AaranWang closed 4 weeks ago
9
Reproducibility issues - Different scores than the ones from ProteinGym

#33 geduran closed 3 weeks ago
7
How to use my own dataset

#32 Colin-Jay closed 1 month ago
5
'utf-8' codec can't decode byte 0x80 in position 64: invalid start byte

#31 tmai-juv closed 1 month 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 1 month ago
1
Add missing import

#29 memgonzales closed 2 months ago
1
per residue representations

#28 FlorianWieser1 closed 2 months ago
2
Mismatch between ESM2 pretraining dataset and SaProt pretraining dataset

#27 ItamarChinn closed 2 months ago
1
Finetuning GPU memory cost

#26 byte233 closed 2 months ago
2
Foldseek can't be used

#25 huanggewudi closed 3 months ago
4
pretraining esm2_t33_650M_UR50D

#24 yufengwhy closed 3 months ago
3
EC GO results

#23 Heisenburger2020 closed 2 months ago
3
Why is the length of the SA-token sequence not equal to the length of the model outputs?

#22 NAME76 closed 3 months ago
1
The length of the Metal Ion Binding dataset is different from that in the paper

#21 mikochou closed 3 months ago
2
The meaning of output size

#20 Yangqy-16 closed 3 months ago
2
Downstream Annotation task 'EC/GO' finetuning overfitting

#19 CiaoHe closed 3 months ago
3
Setting my configuration to for SaProt_650M_AF2

#18 WillHarrigan closed 3 months ago
1
Release code about Contact Head prediction and evaluation

#17 CiaoHe closed 3 months ago
2
Unable to Open Downstream Task MDB Files in Access After Downloading from GitHub Tutorial

#16 RenQiuhan closed 4 months ago
2
Additional input values generated by the tokenizer

#15 tpritsky closed 4 months ago
5
Getting protein embeddings

#14 memgonzales closed 4 months ago
5
Wrong link to hugging face model

#13 jahnzh closed 6 months ago
1
Some weights of EsmModel were not initialized from the model checkpoint

#12 toooooodo closed 6 months ago
2
Back Translate 3Di Tokesn to PDB Format

#11 mahdip72 closed 5 months ago
5
Clarification Needed on Data Types

#10 Finnyear closed 7 months ago
1
ClinVar query

#9 nrafaili closed 7 months ago
2
model for Fine-tune SaProt.

#8 jskim217 closed 7 months ago
0
missing pad_sequences

#7 igortru closed 8 months ago
0
Fine-tune dataset access

#6 lhallee closed 8 months ago
2
License

#5 RaulFD-creator closed 8 months ago
2
Fine-tuned model weights

#4 prihoda closed 8 months ago
5
dynamic model/dataset selection is not working

#3 igortru closed 8 months ago
11
Using ProstT5 or EsmFold to predict foldseek tokens?

#2 igortru closed 8 months ago
77
Pretraining dataset

#1 lhallee closed 9 months ago
2