samsledje D-SCRIPT issues

samsledje / D-SCRIPT

A structure-aware interpretable deep learning model for sequence-based prediction of protein-protein interactions

http://dscript.csail.mit.edu

MIT License

87 stars 18 forks source link

issues

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how to generate the contact map figure of each prediction protein pair?

#73 20182531027 opened 1 week ago
0
If i download the model(*.pt) file, where should I place the file in order for it to read

#72 20182531027 opened 2 weeks ago
5
Is the Bepler & Berger's language pre-trained model also trained along with the rest of Topsy-Turvy modules?

#71 Twim17 closed 3 weeks ago
1
dscript predict doesn't batch candidates, could be sped up 100s of times

#70 samsledje opened 1 month ago
0
Add HuggingFace support

#69 samsledje closed 1 month ago
0
The size of tensor a (4268) must match the size of tensor b (2000) at non-singleton dimension 2

#68 Lsz-20 closed 3 months ago
1
dscript extract-3di only extracts one sequence per input file

#67 Ale-Rossi opened 5 months ago
0
Can't get attribute '_rebuild_parameter_with_state'

#66 Rohit-Satyam closed 7 months ago
8
Queries about sequence identity in the dataset

#65 sirius777coder closed 7 months ago
3
Using D-SCRIPT for organisms not present in training set

#64 Rohit-Satyam closed 7 months ago
1
Running with n_jobs = -1 throttles all CPU on the machine

#63 samsledje opened 9 months ago
0
predictions error with nonTT3D and TT3D

#62 dp9090 closed 7 months ago
1
proteinA x proteinB skipped (The size of tensor a (2581) must match the size of tensor b (2000)

#61 zhijs closed 7 months ago
2
ModuleNotFoundError when trying to unload pretrained TT3D model

#60 SarahND97 closed 7 months ago
5
R notebooks added for baseline sequence-based analysis

#59 kap-devkota closed 1 year ago
0
How to train D-SCRIPT end-to-end?

#58 DragonDescentZerotsu closed 1 year ago
1
how to compare TT3D contact map to AlphaFold multimer prediction?

#57 twaksman001 opened 1 year ago
0
Using D-SCRIPT in slurm

#56 CuiChangIsLaJi closed 1 year ago
1
TT3D - error at beginning of making predictions

#55 twaksman001 closed 1 year ago
1
extract-3di command fail

#54 twaksman001 closed 1 year ago
10
Optimization Parameter Causes Exceptions In Predictions

#53 merterden98 opened 1 year ago
0
TT3D - files?

#52 twaksman001 closed 1 year ago
0
Tt3d predict: Update predict CLI to incorporate 3Di .fasta file

#51 samsledje closed 1 year ago
0
Update requirements.txt

#50 samsledje closed 1 year ago
0
'collections.OrderedDict' object has no attribute cuda

#49 Moeinh77 closed 1 year ago
1
The API docs is incomplete for prediction

#48 Moeinh77 closed 1 year ago
1
Kapil fseek+opt

#47 kap-devkota closed 1 year ago
1
Test dataset construction

#46 igwill closed 1 year ago
3
Using d-script with complexes

#45 Moeinh77 closed 1 year ago
1
Modify model.predict to have consistent signature with model.map_predict (include foldseek stuff)

#44 samsledje closed 1 year ago
0
Added foldseek branch

#43 samsledje closed 1 year ago
0
Update dev-contacts with commits from main

#42 samsledje closed 2 years ago
1
Fix/update pretrained & Issue #35

#41 samsledje closed 2 years ago
1
Confusions about embedding dimensions

#40 xingyu617 closed 2 years ago
1
Some consultation on calculating contact map (label)

#39 EityXiao closed 2 years ago
1
Create automatic test runner

#38 samsledje closed 2 years ago
0
Added typing documentation & automatic retrying for corrupted models

#37 merterden98 closed 2 years ago
0
pretrained file for embed

#36 jfwu-ai closed 2 years ago
2
Update `dscript.language_model` to use h5py `require_dataset` instead of `create_dataset`

#35 samsledje closed 2 years ago
0
fix: added biopython as dependency in setup.py

#34 merterden98 closed 2 years ago
1
D-SCRIPT 0.2.0 -- Topsy-Turvy

#33 samsledje closed 2 years ago
0
Could you provide the script of processing Hwang et al.’s benchmark dataset of docked protein structures?

#32 paive closed 2 years ago
1
In the .fasta file, multiple proteins share the same sequence.

#31 LtECoD closed 2 years ago
1
Same protein pairs but have different labels

#30 YanjunLi-CS closed 2 years ago
3
prediction error

#29 hujingchu closed 2 years ago
5
What is the purpose of the argument dumb-embed-switch?

#28 redsphinx closed 2 years ago
3
SkipLTSM object has no attribute 'map_predict'

#27 777moneymaker closed 2 years ago
1
Data request: pre-computed PPIs

#26 lcscs12345 closed 2 years ago
4
Prediction Quality of the human_v1.sav model

#25 Mike1359 closed 3 years ago
1
Cannot reproduce the paper results using default training hyperparameters

#24 xueeinstein closed 2 years ago
7