HADDOCK

All

70 repositories

haddocking.github.io
Public
Webpage of the Bonvinlab @ Utrecht University and HADDOCK software
education research structural-biology modeling software protein-protein-interaction structural-bioinformatics integrative-modeling utrecht-university
HTML
•
MIT License
•22•13•2•4•Updated Sep 19, 2025Sep 19, 2025
powerfit
Public
Rigid body fitting of atomic strucures in cryo-electron microscopy density maps
gpu cryo-em utrecht-university python
Python
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Apache License 2.0
•9•22•15•5•Updated Sep 18, 2025Sep 18, 2025
protein-detective
Public
Python package to detect proteins in EM density maps.
Python
•
Apache License 2.0
•0•0•3•2•Updated Sep 18, 2025Sep 18, 2025
haddock3
Public
Official repo of the modular BioExcel version of HADDOCK
bioinformatics proteins modelling docking workflows complexes integrative-modeling utrecht-university
Python
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Apache License 2.0
•51•188•15•7•Updated Sep 18, 2025Sep 18, 2025
BM5-clean
Public
Docking benchmark 5 - cleaned and ready to use for HADDOCK
benchmark proteins modelling docking haddock complexes utrecht-university capri
Roff
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Apache License 2.0
•6•14•0•0•Updated Sep 17, 2025Sep 17, 2025
haddock-restraints
Public
Generate restraints to be used in HADDOCK
rust bioinformatics structural-biology webassembly computational-biology haddock tbl protein-docking restraints
Rust
•
MIT License
•2•5•2•0•Updated Sep 17, 2025Sep 17, 2025
haddock-tools
Public
Set of useful HADDOCK utility scripts
structural-biology haddock integrative-modeling utrecht-university computational-structural-biology python
Python
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Apache License 2.0
•19•54•0•0•Updated Sep 15, 2025Sep 15, 2025
haddock3-user-manual
Public
Apache License 2.0
•2•1•1•1•Updated Sep 11, 2025Sep 11, 2025
protein-quest
Public
Python package to search/retrieve/filter proteins and protein structures
Python
•
Apache License 2.0
•0•1•2•2•Updated Sep 10, 2025Sep 10, 2025
haddock-runner
Public
Run large scale HADDOCK simulations using multiple input molecules in different scenarios
benchmark bioinformatics structural-biology high-performance-computing haddock large-scale utrecht-university
Go
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Apache License 2.0
•2•5•2•0•Updated Sep 9, 2025Sep 9, 2025
haddock-pilot
Public
HADDOCK pilot machinery for running on HPC systems
Shell
•
Apache License 2.0
•0•0•0•0•Updated Sep 8, 2025Sep 8, 2025
prodigy
Public
Predict the binding affinity of protein-protein complexes from structural data
bioinformatics python3 utrecht-university binding-affinity
Python
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Apache License 2.0
•30•146•1•1•Updated Sep 2, 2025Sep 2, 2025
haddock3-webapp
Public
Web app which is front-end for bartender and wraps workflow builder with haddock3 catalog
TypeScript
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Apache License 2.0
•1•0•0•0•Updated Aug 29, 2025Aug 29, 2025
deeprank-gnn-esm
Public
Graph Network for protein-protein interface including language model features
Python
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Apache License 2.0
•5•7•2•1•Updated Aug 6, 2025Aug 6, 2025
arctic3d
Public
Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
data-mining clustering data-retrieval utrecht-university pdbe-s-rest-api protein-docking macromolecular-modeling
Python
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Apache License 2.0
•6•31•3•7•Updated Aug 1, 2025Aug 1, 2025
pdb-tools
Public
A dependency-free cross-platform swiss army knife for PDB files.
bioinformatics structural-biology pdb protein structural-bioinformatics utrecht-university rcsb python
Python
•
Apache License 2.0
•117•427•19•7•Updated Jul 21, 2025Jul 21, 2025
haddock-restraints-wasm
Public
Rust
•
Apache License 2.0
•0•0•0•0•Updated Jul 9, 2025Jul 9, 2025
nanobodies
Public
Python
•
Apache License 2.0
•0•1•0•0•Updated Jun 30, 2025Jun 30, 2025
cport
Public archive
CPORT is a Consensus Prediction Of interface Residues in Transient complexes used to predict protein-protein interface residues.
machine-learning bioinformatics deep-neural-networks deep-learning computational-biology protein-protein-interaction predictor utrecht-university research-software meta-predictor
Python
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Apache License 2.0
•3•2•5•3•Updated Jun 9, 2025Jun 9, 2025
alphaflow-antibodies
Public
Python
•
Apache License 2.0
•1•2•0•0•Updated May 26, 2025May 26, 2025
powerfit-tutorial
Public
Simple tutorial to showcase the use of PowerFit.
Shell
•1•2•0•1•Updated May 8, 2025May 8, 2025
.github
Public
0•0•0•0•Updated May 7, 2025May 7, 2025
haddock3-paper-data
Public
HTML
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Apache License 2.0
•0•1•0•0•Updated Apr 29, 2025Apr 29, 2025
DNA-ligand-benchmark
Public
DNA - ligand docking benchmark and associated scripts
Apache License 2.0
•0•0•0•0•Updated Apr 25, 2025Apr 25, 2025
fandas
Public
Prediction of ssNMR spectra from structure
nmr chemical-shifts utrecht-university solid-state-nmr spetroscopy
Python
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Apache License 2.0
•0•2•5•1•Updated Feb 28, 2025Feb 28, 2025
binding-affinity-benchmark
Public
Protein-protein binding affinity benchmark
Python
•
Apache License 2.0
•4•15•0•0•Updated Feb 14, 2025Feb 14, 2025
proABC-2
Public
Deep learning framework to predict antibody paratope residues
Python
•
Apache License 2.0
•3•3•0•0•Updated Feb 7, 2025Feb 7, 2025
protein-glycans
Public
Python
•
Apache License 2.0
•0•4•0•0•Updated Dec 4, 2024Dec 4, 2024
prodigy-lig
Public
Prediction of Protein-Small molecule binding affinities
python bioinformatics prediction utrecht-university small-molecule
Python
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Apache License 2.0
•5•17•0•0•Updated Oct 14, 2024Oct 14, 2024
protein-peptide
Public
Protein-peptide HADDOCK-ready docking benchmark
Apache License 2.0
•1•2•0•0•Updated Sep 5, 2024Sep 5, 2024