Issues

• [BUG] --num-model-seeds 1 runs at seed 2746317213, not the default seed 42 (seeds derived from hardcoded start_seed = 42, override not logged)

  aqlaboratory/openfold-3#435 · Filter by author OtoYuki opened on Oct 3, 2026

• [BUG] Save templates at the end of an inference run

  bugdata preprocessing
  aqlaboratory/openfold-3#428 · Filter by author jnwei opened on Sep 25, 2026
  1

• Add template processing and fetching to the align-msa-server command

  enhancementgood first issue
  aqlaboratory/openfold-3#427 · Filter by author jnwei opened on Sep 25, 2026
  1

• Add option --norun_inference to simplify precomputing MSA and templates from Colabfold server

  enhancement
  aqlaboratory/openfold-3#421 · Filter by author tomgoddard opened on Sep 18, 2026
  2

• Unable to reproduce the OpenBind-0 RnP2025-preview results end to end from the released inputs

  enhancementscience
  aqlaboratory/openfold-3#413 · Filter by author HBioquant opened on Sep 16, 2026
  3

  

• [BUG] CIF Direct Template - Template coordinates are NEVER used, fetched from RCSB or dropped altogether

  bug
  aqlaboratory/openfold-3#406 · Filter by author aqemia-antonin-brossollet opened on Sep 14, 2026
  5

  

• [BUG] Paired MSA truncation ranks rows with an int64 product that silently overflows

  bugdata preprocessingneeds-triage
  aqlaboratory/openfold-3#372 · Filter by author ljarosch opened on Aug 16, 2026
  3

• Allow residue/component identifier specification for SMILES input.

  contributions welcomeenhancementgood first issue
  aqlaboratory/openfold-3#323 · Filter by author roccomoretti opened on Jul 20, 2026
  1

• Requesting per-atom pLDDT (and optionally PAE / resolved-prediction) for the RNA distillation set

  enhancementscience
  aqlaboratory/openfold-3#316 · Filter by author KOarch opened on Jul 17, 2026
  8

  

• [MASTER ISSUE] dataset building toward finetuning cache

  bugneeds-triage
  aqlaboratory/openfold-3#278 · Filter by author JenkeScheen opened on Jun 25, 2026
  4

• Inference OOM from get_token_frame_atoms

  bugenhancementinference
  aqlaboratory/openfold-3#225 · Filter by author GMNGeoffrey opened on May 19, 2026
  2

• Support covalently bound ligands in inference

  enhancementscience
  aqlaboratory/openfold-3#219 · Filter by author gilep opened on May 11, 2026
  1

• Restoring chunking for batch_size > 1 with optimized kernels

  enhancement
  aqlaboratory/openfold-3#206 · Filter by author GMNGeoffrey opened on Apr 30, 2026
  6

  

• [BUG] prep_cutlass() in _deepspeed_evo_attn breaks DeepSpeed Evoformer attention on AMD/ROCm

  buginference
  aqlaboratory/openfold-3#177 · Filter by author dbjoreli opened on Apr 13, 2026
  4

  

• [QUESTION] Conformer random initialization

  bugneeds-triagescience
  aqlaboratory/openfold-3#162 · Filter by author andrewliu2001 opened on Apr 1, 2026
  1

• [QUESTION] Cyclic protein prediction with covalent bonds?

  enhancementscience
  aqlaboratory/openfold-3#161 · Filter by author dimi-swiftpharma opened on Mar 31, 2026
  2

• [BUG] planar sp2 C=C bond giving a 3D geometry

  bugmodelscience
  aqlaboratory/openfold-3#136 · Filter by author jandom opened on Mar 17, 2026
  8

• [BUG] Custom CCD is not properly read

  buginferencescience
  aqlaboratory/openfold-3#109 · Filter by author ljarosch opened on Feb 3, 2026
  

• [BUG] Cuda Out of Memory on large structure even low_mem is set

  buginference
  aqlaboratory/openfold-3#71 · Filter by author xraywu opened on Dec 11, 2025
  4

• [BUG] SLURM autodetection causes OF3 to hang on compute cluster

  buginferenceOpenFold Consortium Member
  aqlaboratory/openfold-3#47 · Filter by author reedharrison opened on Nov 19, 2025
  5

• [BUG] Template alignments skipped after processing.

  bugcontributions welcomedata preprocessingOpenFold Consortium Member
  aqlaboratory/openfold-3#43 · Filter by author halasadi opened on Nov 14, 2025
  4

  

• [BUG][Documentation gap] Template alignments skipped in preprocessing. Request details on input .sto requirements.

  bugdata preprocessingdocumentationOpenFold Consortium Membertraining
  aqlaboratory/openfold-3#42 · Filter by author ECalfeeAdaptive opened on Nov 14, 2025
  5

  

• [documentation gap] - Minimum requirements, what is the tradeoff when you use low mem mode

  documentationInstallationmodelOpenFold Consortium Member
  aqlaboratory/openfold-3#25 · Filter by author smlewis opened on Nov 3, 2025
  3

  

• Thank you!

  aqlaboratory/openfold-3#13 · Filter by author lucajovine opened on Oct 28, 2025
  1