google-deepmind/alphafold

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Open source code for AlphaFold 2.

Stars: 14.9k
Forks: 2.9k
Open beginner issues: 0
Indexed issues: 277

Dominant language: Python
License: Apache-2.0
Last GitHub push: Apr 22, 2026
Latest indexed: Sep 16, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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277 open issues indexed

Option to run AlphaFold-multimer with the two monomers already folded Open

feature request

google-deepmind/alphafold#235 · 1 comment · 6 reactions · 0 assignees · Indexed Sep 16, 2026
Improper chain IDs when running Multimer model Open

error report

google-deepmind/alphafold#251 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Question on inputting as PDB/structure files rather than .fasta for multimer predictions Open

feature request

google-deepmind/alphafold#279 · 3 comments · 4 reactions · 0 assignees · Indexed Sep 16, 2026
High TM-score (91.3) and well-matched result but with very low DockQ value (0.05) Open

usage question

google-deepmind/alphafold#297 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Details regarding self-distillation Open

usage question

google-deepmind/alphafold#350 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Modelling and docking a single protein while providing .pdb for the remaining multimer Open

feature request

google-deepmind/alphafold#352 · 1 comment · 4 reactions · 0 assignees · Indexed Sep 16, 2026
executable file not found in $PATH: unknown. Open

cuda

google-deepmind/alphafold#374 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Can I put restraints on the predicted structures? Open

usage question

google-deepmind/alphafold#385 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
about MSA sampling for self-distillation samples Open

usage question

google-deepmind/alphafold#391 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
About the memory consumption on training and inference Open

usage question

google-deepmind/alphafold#397 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
A question about direction of x-axis in backbone frame construction Open

usage question

google-deepmind/alphafold#400 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
On docker after some time: No compatible CUDA device is available Open

cuda docker

google-deepmind/alphafold#403 · 11 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
non-docker AF2 on HPC cannot use GPU xla_bridge.py:257] No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.) Open

google-deepmind/alphafold#409 · 1 comment · 2 reactions · 0 assignees · Indexed Sep 16, 2026
Job was killed with `/app/run_alphafold.sh: line 3: 8 Killed python /app/alphafold/run_alphafold.py "$@"`` Open

google-deepmind/alphafold#425 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Use of use_precomputed_msas Open

google-deepmind/alphafold#427 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Inference multiple protein structure with single compilation Open

google-deepmind/alphafold#428 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
How to align chain ID of two complexes before running DockQ? Open

google-deepmind/alphafold#434 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
the setting of interface_fape loss is different with paper description Open

google-deepmind/alphafold#435 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Faster MSA computations with chunked DBs on Colab Open

google-deepmind/alphafold#437 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 16, 2026
python run_docker.py --helpshort|grep 'num_multimer_predictions_per_model' --num_multimer_predictions_per_model: How many predictions (each with a Open

google-deepmind/alphafold#445 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Running alphafold on masks Open

google-deepmind/alphafold#449 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Can I run alphafold2 without any structure template information? Open

google-deepmind/alphafold#457 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Only use Structure module to predict structure with given representations Open

google-deepmind/alphafold#461 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
issues with uniprot.fasta file integrity when returning jackhmmer results Open

third-party tool

google-deepmind/alphafold#467 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Extracting single representation from predictions Open

usage question

google-deepmind/alphafold#471 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Jackhmmer failed without error message Open

third-party tool

google-deepmind/alphafold#477 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Unfolded regions in big multimers Open

usage question

google-deepmind/alphafold#480 · 5 comments · 1 reaction · 0 assignees · Indexed Sep 16, 2026
runtime Error: Open

colab duplicate relax

google-deepmind/alphafold#482 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Increasing Number of Ranked pdb outputs on monomer Open

google-deepmind/alphafold#484 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Tensor cores or cuda cores? Open

google-deepmind/alphafold#485 · 21 comments · 2 reactions · 0 assignees · Indexed Sep 16, 2026
Alphafold arguments Open

usage question

google-deepmind/alphafold#495 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Unable to initialize backend 'gpu' Open

google-deepmind/alphafold#498 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
intermediate strucutures Open

google-deepmind/alphafold#506 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 16, 2026
Running specific monomer models on alphafold 2.2 Open

google-deepmind/alphafold#521 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
HHSearch fails on large predicted protein Open

google-deepmind/alphafold#522 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
clarification of pTM/ipTM scores in AF multimer Open

google-deepmind/alphafold#524 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Terminal shutdown Open

usage question

google-deepmind/alphafold#529 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 16, 2026
Does alphafold support proteins with non-canonical aminoacids such as selenocysteine? Open

usage question

google-deepmind/alphafold#531 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
ETL (msa+templates) should be separated from inference Open

feature request

google-deepmind/alphafold#542 · 2 comments · 1 reaction · 0 assignees · Indexed Sep 16, 2026
Ver2.2.0 ValueError: The number of positions must match the number of atoms Open

relax

google-deepmind/alphafold#543 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Modeling with a defined template Open

feature request usage question

google-deepmind/alphafold#546 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Increased memory usage while folding multiple proteins one after another Open

google-deepmind/alphafold#549 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 16, 2026
Pushd and popd commands still haven't been removed from download scripts on the main branch. Open

setup

google-deepmind/alphafold#557 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Ask for a question about how to using AlphaFold Protein Structure Database to calculate the RSA? Open

afdb usage question

google-deepmind/alphafold#561 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
AlphaFold Multimer v2.2.2 Incorrectly Predicts Homo-oligomer Despite PDB Structure Open

google-deepmind/alphafold#572 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Can we limit the depth of the MSA? Open

feature request usage question

google-deepmind/alphafold#579 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 16, 2026
models variability for AF multimer Open

google-deepmind/alphafold#585 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Rescoring and Constraints in multimer modeling. Open

google-deepmind/alphafold#586 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
one error about alphafold，ask for help online Open

google-deepmind/alphafold#592 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Too many command-line arguments : No space in the command Open

google-deepmind/alphafold#593 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026

google-deepmind/alphafold

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