deepmind/alphafold: Open source code for AlphaFold.

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alphafold Recent Issues

Issue Title State Comments Created Date Updated Date Closed Date
A problem occurred while I was running the Alphafold open 0 2022-11-29 2022-11-23 -
Running Alphafold using unpublished Pdb as a custom template open 0 2022-11-29 2022-11-23 -
Can I customize the database? open 0 2022-11-28 2022-11-23 -
Alphafold Multimer Results open 0 2022-11-27 2022-11-23 -
AlphaFold multimer has name error in the last step open 5 2022-11-26 2022-11-23 -
Alphafold broken on Colab open 1 2022-11-24 2022-11-23 -
Running without MSA features open 0 2022-11-23 2022-11-23 -
AttributeError: 'Config' object has no attribute 'jax_experimental_name_stack' closed 19 2022-11-22 2022-11-23 2022-11-28
AlphaFold Colab crashing at cell 5 closed 3 2022-11-22 2022-11-23 2022-11-28
A question about running time on MSA open 0 2022-11-20 2022-11-23 -
How to accelerate protein prediction open 3 2022-11-16 2022-11-23 -
Pickle output result_model_1_multimer_v2_pred_0.pkl has a JAX dependency open 4 2022-11-16 2022-11-23 -
An error occurred while downloading the database open 0 2022-11-11 2022-11-23 -
Erros while predicting the structures closed 2 2022-11-10 2022-11-23 2022-11-10
`template_domain_names` missing in features.pkl on multimer mode. open 0 2022-11-10 2022-11-23 -
AlphaFold multimer mode crashes with lower case protein sequences but not upper case protein sequences open 1 2022-11-09 2022-11-23 -
Illegal character in pub_seqres.txt database file open 3 2022-11-03 2022-11-23 -
Locally install and run AlphaFold open 2 2022-11-02 2022-11-23 -
compare the predicted and actual structure? open 0 2022-11-01 2022-11-23 -
docker build -f docker/Dockerfile -t alphafold . Build failed open 5 2022-11-01 2022-11-23 -
Do I need to upgrade the database? open 2 2022-10-28 2022-11-23 -
predicting structure of octamer closed 0 2022-10-27 2022-11-23 2022-10-27
Problem with docker build -f docker/Dockerfile -t alphafold . open 6 2022-10-21 2022-11-23 -
GPU Memory Resource Exhaustion issue open 0 2022-10-19 2022-11-23 -
Is there any solution that we can run AF2 by using GCP TPU vm? open 0 2022-10-17 2022-11-23 -
No such file or directory: '.../pdb_mmcif/mmcif_files/XXXX.cif' open 5 2022-10-15 2022-11-23 -
Carriage returns in pdb_seqres.txt open 0 2022-10-07 2022-11-23 -
Running "run_docker.py" says ModuleNotFoundError: No module named 'asbl' closed 1 2022-10-06 2022-11-23 2022-10-06
Link format for downloading pdb files from a third party application open 0 2022-10-06 2022-11-23 -
Port to Metal and macOS open 0 2022-10-04 2022-11-23 -
GPU is not fully used. open 0 2022-10-01 2022-11-23 -
Can I use cudatoolkit==11.7.0 instead of cudatoolkit==11.1.1 ? closed 1 2022-09-29 2022-11-23 2022-09-30
difference of results between locally run alphafold and alphafold colab open 9 2022-09-26 2022-11-23 -
A more general fasta file parser open 0 2022-09-25 2022-11-23 -
How does AlphaFold2 determine the protonation state/hydrogen open 0 2022-09-22 2022-11-23 -
Multimer predictions degraded after updating from 2.2.3 to 2.2.4? open 30 2022-09-22 2022-11-23 -
AttributeError: module 'jax' has no attribute 'tree_multimap' closed 2 2022-09-19 2022-11-23 2022-09-20
Too many command-line arguments : No space in the command open 2 2022-09-16 2022-11-23 -
one error about alphafold,ask for help online open 0 2022-09-15 2022-11-23 -
AlphaFold (or hmmsearch) is not able to parse some pdb_seqres.txt due to unusual residue naming closed 2 2022-09-14 2022-12-01 2022-09-19
How to get pdb structure files in bulk download from Google Cloud closed 1 2022-09-09 2022-11-23 2022-09-12
New Jax version broke Alphafold on Colab? closed 12 2022-09-07 2022-11-30 2022-09-21
Low GPU memory-usage and 0 GPU-Util open 1 2022-09-06 2022-11-23 -
Alphafold2 Modulenotfound closed 5 2022-09-02 2022-11-23 2022-10-03
Rescoring and Constraints in multimer modeling. open 0 2022-09-01 2022-11-23 -
models variability for AF multimer open 0 2022-09-01 2022-11-23 -
inquiry regarding input format open 0 2022-09-01 2022-11-23 -
Different output from the same sequence closed 2 2022-08-30 2022-11-23 2022-09-13
protein protein interaction Indexeror open 7 2022-08-29 2022-11-23 -
Can we limit the depth of the MSA? open 1 2022-08-25 2022-11-23 -