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HADDOCK submission

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If one of your molecules is DNA/RNA, restraints are automatically created to preserve its structure. Uncheck this option if you are docking with unstructured DNA/RNA.

HADDOCK deletes by default all hydrogens except those bonded to a polar atom (N, O). Uncheck this option if you have NOEs or other specific restraints to non-polar hydrogens.

Random patches

Center of mass restraints



Surface contact restraints


Random exclusion


Radius of gyration restraint












Solvated docking mode

Cutoff for defining neighbouring flexible regions





In addition to distance restraints, you may specify dihedral and hydrogen bond restraints. These restraints can be inter- or intra-molecular.







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Define the weights for the various terms for the sorting of structures (scoring)
1: Rigid body EM (it0)
2: semi-flexible SA (it1)
3: water refinement



Energy constants per stage




Define the weights for the various terms for the sorting of structures (scoring)
1: Rigid body EM (it0)
2: semi-flexible SA (it1)
3: water refinement



Energy constants per stage




Define the weights for the various terms for the sorting of structures (scoring)
1: Rigid body EM (it0)
2: semi-flexible SA (it1)
3: water refinement



Energy constants per stage




Energy constants for dihedral angle restraints





Energy constants for radius-of-gyration restraints










SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











SANI energy constants


Energy constants per stage






VEAN energy constants

ini_bor energy constants per stage





fin_bor energy constants per stage





ini_cen energy constants per stage





fin_bor energy constants per stage











PCS energy constants


Energy constants per stage











PCS energy constants


Energy constants per stage











PCS energy constants


Energy constants per stage











PCS energy constants


Energy constants per stage











PCS energy constants


Energy constants per stage











PCS energy constants


Energy constants per stage











PCS energy constants


Energy constants per stage











PCS energy constants


Energy constants per stage











PCS energy constants


Energy constants per stage











PCS energy constants


Energy constants per stage











PCS energy constants


Energy constants per stage












DANI energy constants


Energy constants per stage














DANI energy constants


Energy constants per stage














DANI energy constants


Energy constants per stage














DANI energy constants


Energy constants per stage














DANI energy constants


Energy constants per stage














DANI energy constants


Energy constants per stage














DANI energy constants


Energy constants per stage














DANI energy constants


Energy constants per stage














DANI energy constants


Energy constants per stage














DANI energy constants


Energy constants per stage














DANI energy constants


Energy constants per stage













Do you want to include the electrostatic energy term for docking? Note that it will be automatically included in the solvent refinement





Epsilon constant for the electrostatic energy term. Note that for explicit solvent refinement cdie with epsilon=1 is used.



Scaling of intermolecular interactions for semi-flexible SA (it1)

Initial value




Final value



Define the weights for the various terms for the sorting of structures (scoring)
1: Rigid body EM (it0)
2: semi-flexible SA (it1)
3: water refinement

Evdw




Eelec




Eair




Erg




Esani




Exrdc




Expcs




Edani




Evean




Ecdih




Esyn




BSA




dEint




Edesolv




cryoEM



Do you want to cross-dock all combinations in the ensembles of starting structures?
Turn off this option if you only want to dock structure 1 of ensemble A to structure 1 of ensemble B, structure 2 to structure 2, etc.


Enable the next option to multiply the number of structures in all iterations by the number of starting structure combinations.
The number of combinations depends on the cross-docking parameter.
If cross-docking is disabled, the number of combinations is the size of the first ensemble.
If cross-docking is enabled, the number of combinations is the sizes of all ensembles multiplied.







it1 parameters
















Final solvated refinement



Solvated docking can be enabled in the Sampling Parameters section

Which method to use for solvating?
db: database-based (recommended), restraints: for restrained solvating to amino-acid most often forming

Which propensity database to use?
Statistical: based on an analysis of water-mediated contacts in the PDB, Kyte-Doolittle: based on the Kyte-Doolittle hydrophobicity scale




This is the fraction of all interface water after the initial rigid body docking that will be kept (note that more waters might be removed if the interaction energy is unfavorable)

This is the fraction of interface water involving DNA phosphates after the initial rigid body docking that will be kept (note that more waters might be removed if the interaction energy is unfavorable)










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This work is co-funded by the Horizon 2020 projects EOSC-hub and EGI-ACE (grant numbers 777536 and 101017567), BioExcel (grant numbers 823830, 675728 and 101093290)
and by a computing grant from NWO-ENW (project number 2019.053).