Issues

• Add proper regression test option using the examples test config files

  CI / repositoryenhancement
  haddocking/haddock3#1731 · Filter by author amjjbonvin opened on Oct 17, 2026

• Add a test to check that CNS scripts present in various modules are matching

  enhancement
  haddocking/haddock3#1729 · Filter by author amjjbonvin opened on Oct 15, 2026
  

• Ten glycosylation patches are never applied: alpha O-glycans (Tn antigen), Cys S-glycans and all L-sugar variants go undetected

  bugm|topoaaparameters-topologies
  haddocking/haddock3#1718 · Filter by author amjjbonvin opened on Oct 9, 2026

• Duplicate PRESidue definitions in carbohydrate.top, and the second B1SL bonds to Thr OG1

  bugparameters-topologies
  haddocking/haddock3#1717 · Filter by author amjjbonvin opened on Oct 9, 2026

• A26S and A28S restrain a non-existent -O5, leaving SIA C2 with no chirality restraint

  bugparameters-topologies
  haddocking/haddock3#1716 · Filter by author amjjbonvin opened on Oct 9, 2026

• Add log normal distance restraining function

  CNScommunityenhancementm|emrefm|flexrefm|mdrefm|rigidbody
  haddocking/haddock3#1713 · Filter by author amjjbonvin opened on Oct 9, 2026
  

• We want caching!

  enhancementplanned-long-term
  haddocking/haddock3#1689 · Filter by author AnnaEngel98 opened on Sep 3, 2026
  

• Add protein-RNA example to haddock3/examples

  examplesplanned-long-term
  haddocking/haddock3#1683 · Filter by author AnnaKravchenko opened on Sep 1, 2026
  

• Hardcoded md timestep - is it intenional?

  m|mdrefm|mdscoringquestion
  haddocking/haddock3#1680 · Filter by author AnnaKravchenko opened on Sep 1, 2026
  1

• Restrict libparallel scheduler exception handling to expected task failures

  bug
  haddocking/haddock3#1673 · Filter by author sjdv1982 opened on Aug 28, 2026

• update deeprank module to use upstream v2.0.0

  enhancementm|deeprankplanned-long-term
  haddocking/haddock3#1671 · Filter by author rvhonorato opened on Aug 21, 2026

• refactor modularity-breaking implementations

  planned-long-termrefactoring
  haddocking/haddock3#1530 · Filter by author rvhonorato opened on Apr 21, 2026
  2

• Add caching to store RMSD values

  featureplanned-long-term
  haddocking/haddock3#1528 · Filter by author rvhonorato opened on Apr 21, 2026
  5

• Allow handling of molecules with more than 99999 atoms

  enhancementm|topoaaplanned-long-term
  haddocking/haddock3#1506 · Filter by author amjjbonvin opened on Apr 9, 2026
  7

  

• Enable docking of membrane proteins embedded into a bilayer

  featureplanned-long-term
  haddocking/haddock3#1486 · Filter by author amjjbonvin opened on Mar 4, 2026
  2

  

• Add support for custom alignment file in [caprieval]

  featurem|caprievalplanned-long-term
  haddocking/haddock3#1410 · Filter by author AnnaKravchenko opened on Oct 3, 2025
  3

  

• Add an option to restrain non-canonical NA pairs

  CNScommunityenhancementm|emrefm|flexrefm|mdrefplanned-long-term
  Feature

  haddocking/haddock3#1397 · Filter by author AnnaKravchenko opened on Sep 19, 2025
  3

• Refactor align_full in libnotebooks

  enhancementplanned-long-term
  haddocking/haddock3#1375 · Filter by author AnnaKravchenko opened on Sep 4, 2025
  1

• Refinement workflow output contains cns error file, but workflow is not affected

  bugm|emrefm|flexrefm|mdref
  haddocking/haddock3#1349 · Filter by author AnnaKravchenko opened on Aug 13, 2025
  3

• Analsysis module describing interactions

  enhancementfeatureplanned-long-term
  haddocking/haddock3#1336 · Filter by author VGPReys opened on Jul 29, 2025
  7

  

• Add modules that could add/delete molecules within a workflow

  featureplanned-long-termworkflow
  haddocking/haddock3#992 · Filter by author amjjbonvin opened on Sep 2, 2024
  6

  

• haddock3 workflow without starting with topoaa

  executionplanned-long-term
  haddocking/haddock3#932 · Filter by author VGPReys opened on Jul 10, 2024
  3

  

• Add a saxsscore module.

  featurem|saxsscoreplanned-long-term
  haddocking/haddock3#433 · Filter by author rvhonorato opened on May 16, 2022
  9