Issues

• Glycan leaving-atom removal is name-based (O1), not flag-based: linked ketoses (sialic acids, KDO, fructose, psicose, sorbose, tagatose) get a five-bonded C2

  google-deepmind/alphafold3#752 · Filter by author shahriararab opened on Oct 1, 2026

• chain_ids in summary_confidences.json has one entry per token, not one per chain as documented

  bug
  google-deepmind/alphafold3#746 · Filter by author cindykrafft opened on Sep 23, 2026

• Input.to_json() reorders chains when identical chains are separated by a different chain, so <name>_data.json does not describe the run that produced it

  bug
  google-deepmind/alphafold3#744 · Filter by author cindykrafft opened on Sep 22, 2026

• PAE distribution compresses between 3.0.1 and 3.0.4 on the same af3.bin parameters (protein-RNA-DNA complex)

  question
  google-deepmind/alphafold3#743 · Filter by author shengdar opened on Sep 22, 2026
  1

• Autotuning cache miss for PallasTritonGatedLinearUnit and Inference time increases significantly.

  bug
  google-deepmind/alphafold3#742 · Filter by author Maikuraky opened on Sep 14, 2026
  5

• CCD_6MZ (N6-methyladenosine) RNA modification causes AlphaFold Server jobs to fail; other RNA modifications unaffected

  google-deepmind/alphafold3#739 · Filter by author BhakhriHarsh opened on Sep 6, 2026

• Feature proposal: explicit input preflight validation mode

  enhancement
  google-deepmind/alphafold3#732 · Filter by author sylvesterkaczmarek opened on Aug 31, 2026

• Incorrect layout conversion of ref_space_uid in atom cross-attention

  google-deepmind/alphafold3#730 · Filter by author kilianmandon opened on Aug 26, 2026
  1

• Slow featurization when running inference for same input with multiple seeds

  enhancement
  google-deepmind/alphafold3#675 · Filter by author y1zhou opened on May 21, 2026
  5

• AF3 runtime higher than reported for pool of proteins with 5000 tokens

  question
  google-deepmind/alphafold3#609 · Filter by author karchern opened on Jan 30, 2026
  15

• AF3 cannot predict correct ligand isomer even using userCDD

  question
  google-deepmind/alphafold3#527 · Filter by author antonielgomes opened on Sep 26, 2025
  4

• Unified memory for extra large systems - rematerialization problems

  question
  google-deepmind/alphafold3#432 · Filter by author GorgetteGorg opened on May 28, 2025
  10

• Adding Docker image to container registry

  enhancement
  google-deepmind/alphafold3#322 · Filter by author VRehnberg opened on Feb 24, 2025
  11

• Bond order information missing in output cif files.

  enhancementquestion
  google-deepmind/alphafold3#189 · Filter by author alchemistcai opened on Dec 7, 2024
  3

• AF3 unable to predict covalent bonds between DNA and protein

  enhancement
  google-deepmind/alphafold3#152 · Filter by author alchemistcai opened on Dec 1, 2024
  4

• First issue! Just want to say thank you!

  good first issue
  google-deepmind/alphafold3#1 · Filter by author WillHua127 opened on Nov 11, 2024
  27