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HADDOCK3 - modular integrative modelling software

Authors: Teixeira, Joao; Honorato, Rodrigo; Giulini, Marco; Bonvin, Alexandre; Alidoost, Sarah; Reys, Victor; Jimenez, Brian; +6 Authors

HADDOCK3 - modular integrative modelling software

Abstract

HADDOCK3 2026.8.0 Changes since 2026.7.0. :jigsaw: New Modules Added thedeeprank scoring module - this module scores complexes using deeprank-gnn-esm, a graph neural network that predicts the fraction of native contacts (fnat) between two chains of an interface (#1480) Added thernascan analysis module - this module performs a mutagenesis scan of each RNA base in the interface, following short energy minimisation, and outputs the difference in HADDOCK score between wild-type and mutated models (#1632) :books: New notebooks HADDOCK3 basic protein-DNA notebook (#1629) HADDOCK3 basic protein-glycan notebook (#1630) :beetle: Bug Fixes Corrected ranking in caprieval for reverse sorting - now seletop is adapted to deeprank output (#1622, #1623) Fixed gen_archive crash on non-local filesystems (#1627) Added missing improper for HYP (#1663) Fixed chirality detection by adding (if needed) and keeping HA for all residues (#1637) :broom: Maintenance Added ctrl-c ctrl-v guidelines (#1635) Added workflow module ordering validation (#1651) Full Changelog: https://github.com/haddocking/haddock3/compare/2026.7.0...2026.8.0

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