alphafold_pytorch
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Urinx
An implementation of the DeepMind's AlphaFold based on PyTorch for research
Hi, in order to run a prediction for other target using the alphafold.sh script, I need as input a pkl file, how can I get it?
I have a cyclic peptide sequence. I put it into Alphafold2 Colab, but I didn't get a cyclic peptide structure. What should I do to connect the C-terminal and N-terminal...
After generating features and loading those from the npy file, I'm getting this error when trying to run the alphafold.py script. Any ideas on the cause? RuntimeError: Given groups=1, weight...
I found that an error for some input sequences is produced if an alignment during the feature generation pipeline contains the amino acid place holder X: `KeyError: 'X' Traceback (most...
Hi, I ran feature.sh with T1019s2.seq as input. It generated the files as follows:  But there wasn't T1019s2.pkl or T1019s2.tfrec. Can you tell me how to correctly generate those...
The 'exit' on the line 164 of feature.py produce a lot of problems. When there are more then 1 crop produce that the feature.sh doesn't save the numpy. The first...
Hej, I tried to run plmDCA.m test_data/T1019s2.aln, but I got the following error: octave: no graphical display found octave: disabling GUI features ### N = 88 B_with_id_seq = 393 B...
- How can I get the pkl and tfrec files from the pdb file? - Does not support pdb file? - Please give me the solutions.
- Do you not support other protein besides casp13 dataset? - I want to use covid 19 protein(SARS-CoV-2) on alphafold_casp13 project. Does not support it? - Please give me the...
``` Traceback (most recent call last): File "dataset.py", line 383, in test() File "dataset.py", line 375, in test dataset = ProteinDataset('T1019s2.pkl', DISTOGRAM_MODEL, replica) TypeError: __init__() takes 3 positional arguments but...