lucidrains/alphafold2
To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released
PythonMIT
Issues
- 0
How to adjust the recycling times in model?
#109 opened by Syaoran036 - 4
- 0
read me dimensions are off. Example to run alpha fold 2 msa, and seq lengths should be the same. One is 128, the other is 120.
#104 opened by ofTarradiddle - 0
How can I get the coordinates of all the atoms?
#103 opened by RayTang88 - 1
outerMean module question
#102 opened by ifromeast - 1
- 0
[todo] ensembling
#97 opened by lucidrains - 3
[todo] checkpointing
#81 opened by lucidrains - 4
[todo] BERT loss on MSA
#80 opened by lucidrains - 3
- 2
- 3
[todo] structure module
#93 opened by lucidrains - 1
Missing adding the `relpos` to pairwise-repr `x`
#92 opened by CiaoHe - 1
[todo] recycling
#78 opened by lucidrains - 1
Maybe duplicate residual addition
#91 opened by CiaoHe - 3
TypeError: __init__() got an unexpected keyword argument 'num_backbone_atoms'
#87 opened by jackli777 - 1
- 1
pairwise_repr should be used in rowAttention
#89 opened by CiaoHe - 1
- 4
OuterMean block's typo
#86 opened by CiaoHe - 1
- 1
MSA attention gated problem
#84 opened by CiaoHe - 3
the dimensions of coordinates in CASP12
#71 opened by zhangyi-taotao - 2
[todo] FAPE loss
#79 opened by lucidrains - 2
- 1
[todo] embeddings
#77 opened by lucidrains - 1
[todo] positional encoding
#82 opened by lucidrains - 0
problem with alphafold2/train_pre.py
#76 opened by jackli777 - 2
no coords_3d in train_end2end.py
#73 opened by moonblue333 - 3
MDScaling isn't working right!
#67 opened by xiongzhp - 1
- 3
- 1
test error in utils
#57 opened by lucidrains - 9
CUBLAS ERROR while running example
#49 opened by ychuhp - 5
MSA tensor format
#56 opened by panganqi - 3
- 0
I want use casp13 dataset.
#48 opened by Planet-KIM - 1
the sidechainnet pkg updates, the load function doesnot has parameter return_masks and the format of casp12 data from scn has changed, which is not compatible with train_end2end.py
#51 opened by ditannan - 7
- 1
Link to discord?
#47 opened by ychuhp - 2
- 21
Architecture
#1 opened by lucidrains - 3
Output pdb file
#38 opened by 227BaronChen - 12
center_distogram_torch with center = 'median' breaks when tensors are on CUDA device
#26 opened by lucidrains - 2
How
#30 opened by ErenBalatkan - 0
- 3
- 17
A bug……
#17 opened by 227BaronChen