Issues

• Role of ions in the input file and on the co-folding?

  jwohlwend/boltz#711 · Filter by author MatteoMarengo opened on Oct 23, 2026

• Boltz-2.2.0: Incorrect D-valine stereochemistry and distorted backbone geometry in a cyclic hexapeptide

  jwohlwend/boltz#710 · Filter by author TSC2412 opened on Oct 19, 2026
  2

• Incorrect sign in contact-union gradient causes guidance to ascend the computed potential

  jwohlwend/boltz#708 · Filter by author vv137 opened on Oct 11, 2026

• Are the Boltz-2 affinity training pairs available for overlap checks?

  jwohlwend/boltz#706 · Filter by author tonytu16 opened on Sep 27, 2026

• Non-natural AA peptide (CCD main-chain modifications): distorted covalent bonds, and no configuration gives both correct chemistry and a reliable binding mode

  jwohlwend/boltz#704 · Filter by author sansgordon-lang opened on Sep 16, 2026

• Using the Boltz-2 Affinity Module with a Known Structure

  jwohlwend/boltz#702 · Filter by author MartinFuentetaja opened on Sep 8, 2026

• Question on side chain predictions with given template

  jwohlwend/boltz#701 · Filter by author BJWiley233 opened on Sep 4, 2026
  1

• improve the robustness of the ligand 3D conformation generation

  jwohlwend/boltz#700 · Filter by author AIMedDrug opened on Aug 1, 2026

• Feature request: expose PAE (and confidence JSON) in the hosted API output

  jwohlwend/boltz#697 · Filter by author Ayushmania2002 opened on Jul 17, 2026

• pdb vs mmcif output_format

  jwohlwend/boltz#696 · Filter by author marissadolorfino2024 opened on Jul 9, 2026

• Request for correction: Boltz manifest draft in OpenSciFlow

  jwohlwend/boltz#695 · Filter by author kkkniengLiu opened on Jul 6, 2026

• ConnectTimeoutError to api.colabfold.com when using Boltz --use_msa_server

  jwohlwend/boltz#694 · Filter by author Kj-23 opened on Jun 30, 2026
  2

• ConnectTimeoutErrorwhen fetching fromapi.colabfold.com during high-throughput screening

  jwohlwend/boltz#693 · Filter by author ChenSyyJR opened on Jun 29, 2026
  3

• training code for boltz-2

  jwohlwend/boltz#687 · Filter by author YueZhou-oh opened on May 28, 2026

• Training preprocessing: rcsb.py does not correctly populate cluster_id or msa_id for custom mmCIF datasets

  jwohlwend/boltz#686 · Filter by author ReaganGen opened on May 27, 2026
  1

• [Bug] steering_args['fk_steering'] raises TypeError when steering_args is None (diffusionv2.py:323)

  jwohlwend/boltz#680 · Filter by author Chabname opened on May 13, 2026
  1

• [Bug] pairformer_args.v2 missing from checkpoint hyper_parameters → AttentionPairBias.forward() unexpected kwarg 'k_in'

  jwohlwend/boltz#679 · Filter by author Chabname opened on May 13, 2026
  1

• Boltz2 predictions of ligand poses appear to work well with CCD codes but not well with SMILES strings

  jwohlwend/boltz#678 · Filter by author rjrich opened on May 7, 2026
  2

• Warnings when running boltz2 in a conda environment using an Nvidia RTX A6000 GPU and CUDA 13.2

  jwohlwend/boltz#677 · Filter by author rjrich opened on May 6, 2026

• Installing and Running Boltz2 with CUDA 13.2 and Nvidia RTX A6000 GPU

  jwohlwend/boltz#676 · Filter by author rjrich opened on May 6, 2026
  3

• ACE-CYS cyclization fails

  jwohlwend/boltz#675 · Filter by author Jameel9 opened on Apr 30, 2026
  5

• Predicted structures very different to templates

  jwohlwend/boltz#674 · Filter by author csainzribera opened on Apr 23, 2026

• Error: list index out of range when adding templates in YAML

  jwohlwend/boltz#669 · Filter by author bigsmartguy opened on Apr 6, 2026
  1

• affinity calculation for multiple copies run error

  jwohlwend/boltz#647 · Filter by author quanjm2026 opened on Feb 28, 2026
  3

• Boltz not parsing cif

  jwohlwend/boltz#641 · Filter by author JakobDrumm opened on Feb 9, 2026
  2