HADDOCK3 - modular integrative modelling software

Bug Fixes • Fixed incorrect handling of hetero atoms during CAPRI evaluation, ensuring accurate scoring. • Corrected preprocessing when splitting structures containing MODEL records to avoid malformed inputs. • Added the correct type handling for the seed option in the random_removal command to prevent runtime errors. • Restored missing NGA glycan parameters, resolving issues with glycan-containing systems. • Added a missing example to resolve a reported workflow issue affecting several refinement modules. Enhancements • Added automated topology/parameter generation for unknown small molecules, simplifying preparation of new ligands. • Implemented interface-ligand RMSD–based clustering for protein–ligand examples, improving analysis of docking results. • Added a runtime fallback to the local scheduler when GRID resources are unavailable, improving execution robustness. Examples and Documentation • Added new examples demonstrating workflows and resolving previously reported usage issues. • Expanded example coverage for protein–ligand clustering workflows.