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HADDOCK specifications

Information


Unique identifier OMICS_03778
Name HADDOCK
Alternative name High Ambiguity Driven protein-protein DOCKing
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.2
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Alexandre M.J.J. Bonvin

Publications for High Ambiguity Driven protein-protein DOCKing

HADDOCK citations

 (171)
library_books

Ofatumumab Monoclonal Antibody Affinity Maturation Through in silico Modeling

2018
PMCID: 5889503
DOI: 10.22034/ibj.22.3.180

[…] Docking was performed using Hex 8.0 software, ClusPro 2.0 server[] cluspro (https://cluspro.bu.edu/publications.php), ZDOCK (http://zdock.umassmed. edu/)[], and HADDOCK[] at http://haddock.science.uu.nl/services/HADDOCK 2.2/. This scrutiny was used to determine the interaction and orientation between the two molecules to determine the correct binding between […]

library_books

Prediction of spacer α6 complex: a novel insight into binding of ADAMTS13 with A2 domain of von Willebrand factor under forces

2018
Sci Rep
PMCID: 5893608
PMID: 29636514
DOI: 10.1038/s41598-018-24212-6

[…] imulations,, the present method adopts forced-extended conformations with various lengths from zv-SMD simulations, showing a much more capacity for induced-fit mechanism. The flexible docking program HADDOCK allows full structural flexibility for both side chains and backbone, and may outperform the rigid or semi-flexible docking method in simulating local structural adaption.Interestingly, with o […]

call_split

Cytochrome c speeds up caspase cascade activation by blocking 14 3 3ε dependent Apaf 1 inhibition

2018
PMCID: 5840378
PMID: 29511177
DOI: 10.1038/s41419-018-0408-1
call_split See protocol

[…] Restrained docking calculations were performed with the High Ambiguity Driven Docking approach (HADDOCK)–, using the 3ZCF.pdb structure of Cc and the resulting open model of 14-3-3ε FL from MD calculations. Dielectric constant was set as distance-dependent. Scaling of ambiguous interaction restr […]

library_books

Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1

2018
Sci Rep
PMCID: 5832771
PMID: 29497085
DOI: 10.1038/s41598-018-21952-3

[…] e N- and C-terminal helices of the GAF domain (Supplementary Fig. ). TopDock-predicted residue–residue contacts from each homologous interface were used for restrained docking of the GAF domains with HADDOCK. The docking solutions were pooled and clustered by TopDock, and ranked according to HADDOCK energy, cluster size, distance to cluster centroid, and fulfilment of predicted contacts to select […]

library_books

Solution structure of the cytochrome P450 reductase–cytochrome c complex determined by neutron scattering

2018
PMCID: 5892573
PMID: 29475945
DOI: 10.1074/jbc.RA118.001941

[…] to the experimental data was determined using MultiFoXS () in partial mode where precomputed scattering intensities were used.An initial model for the CPR–cytochrome c complex was produced using the HADDOCK web server () by inputting predicted active interface residues on both the FMN domain and cytochrome c and allowing the program to automatically define peripheral residues. A large number of m […]

library_books

S100B as an antagonist to block the interaction between S100A1 and the RAGE V domain

2018
PLoS One
PMCID: 5812564
PMID: 29444082
DOI: 10.1371/journal.pone.0190545

[…] method can be used to replace S100A1 with mutant-S100A1 (C85S) for NMR experiments without using DTT. We generated the mS100A1-RAGE V domain and S100A1-S100B heterodimeric complex structure using the HADDOCK program [,]. Residues where chosen on each protein interface based on the chemical shift perturbation from the NMR 1H-15N HSQC titration results. All model structures were illustrated using Py […]

Citations

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HADDOCK institution(s)
Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, Utrecht, Netherlands

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