HADDOCK

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74 repositories

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
•56•222•11•4•Updated Feb 13, 2026Feb 13, 2026
DeepRank-Ab
Public
Repository of the DeepRank-Ab AI model and software for scoring antibody-antigen complexes
bioinformatics deep-learning proteins scoring complexes antibodies utrecht-university antigen-antibody-interaction
Python
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Other
•2•17•0•0•Updated Feb 12, 2026Feb 12, 2026
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
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MIT License
•23•13•7•3•Updated Feb 12, 2026Feb 12, 2026
protein-detective
Public
Python package to detect proteins in EM density maps.
Python
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Apache License 2.0
•0•0•2•1•Updated Feb 11, 2026Feb 11, 2026
protein-quest
Public
Python package to search/retrieve/filter proteins and protein structures
Python
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Apache License 2.0
•0•3•5•1•Updated Feb 6, 2026Feb 6, 2026
pdb-tools
Public
A dependency-free cross-platform swiss army knife for PDB files.
python bioinformatics structural-biology pdb protein structural-bioinformatics utrecht-university rcsb
Python
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Apache License 2.0
•121•443•2•2•Updated Feb 3, 2026Feb 3, 2026
HADDOCK-antibody-antigen
Public
Material to run the HADDOCK antibody-antigen modelling protocol
antibody haddock utrecht-university
Python
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Apache License 2.0
•10•23•0•1•Updated Feb 3, 2026Feb 3, 2026
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•6•0•0•Updated Feb 2, 2026Feb 2, 2026
haddock-restraints
Public
Generate restraints to be used in HADDOCK
rust bioinformatics structural-biology webassembly computational-biology haddock tbl protein-docking restraints
Rust
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MIT License
•2•6•0•0•Updated Feb 1, 2026Feb 1, 2026
nanobodies
Public
Python
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Apache License 2.0
•0•3•0•0•Updated Feb 1, 2026Feb 1, 2026
powerfit
Public
Rigid body fitting of atomic strucures in cryo-electron microscopy density maps
python gpu cryo-em utrecht-university
Python
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Apache License 2.0
•10•22•11•1•Updated Jan 28, 2026Jan 28, 2026
alphaflow-antibodies
Public
Python
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Apache License 2.0
•1•2•0•0•Updated Jan 26, 2026Jan 26, 2026
deeprank-gnn-esm
Public
Graph Network for protein-protein interface including language model features
Python
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Apache License 2.0
•5•12•0•0•Updated Jan 22, 2026Jan 22, 2026
arctic3d
Public archive
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•32•0•0•Updated Jan 22, 2026Jan 22, 2026
haddock3-user-manual
Public
Apache License 2.0
•3•1•0•1•Updated Jan 1, 2026Jan 1, 2026
Finetune-Ab
Public
Layer-wise selective Fine-Tuning of protein language models for Antibodies
bioinformatics ai proteins modelling antibodies utrecht-university
Python
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Apache License 2.0
•0•2•0•0•Updated Dec 18, 2025Dec 18, 2025
smiles2pdb
Public
A lightweight C++ command-line tool to convert SMILES strings to PDB files with conformer generation using RDKit
chemistry cpp cheminformatics structural-biology pdb computational-chemistry rdkit drug-design smiles molecular-modeling
C++
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Apache License 2.0
•0•1•0•0•Updated Dec 12, 2025Dec 12, 2025
.github
Public
0•0•0•0•Updated Dec 12, 2025Dec 12, 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 Nov 17, 2025Nov 17, 2025
disvis
Public archive
Visualisation of conformational space restriction by distance restraints
Python
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Apache License 2.0
•9•10•4•0•Updated Nov 7, 2025Nov 7, 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
•34•172•0•0•Updated Oct 3, 2025Oct 3, 2025
haddock-restraints-py
Public
Python bindings for haddock-restraints
Rust
•0•1•0•0•Updated Oct 2, 2025Oct 2, 2025
proABC-2
Public archive
Deep learning framework to predict antibody paratope residues
Python
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Apache License 2.0
•3•4•0•0•Updated Oct 1, 2025Oct 1, 2025
prodigy-cryst
Public
Contacts-based classifier of biological and crystallographic interfaces
python machine-learning bioinformatics structural-biology prediction crystallography utrecht-university
Python
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Apache License 2.0
•4•8•0•0•Updated Oct 1, 2025Oct 1, 2025
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
•6•20•0•0•Updated Oct 1, 2025Oct 1, 2025
haddock-tools
Public
Set of useful HADDOCK utility scripts
python structural-biology haddock integrative-modeling utrecht-university computational-structural-biology
Python
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Apache License 2.0
•19•57•0•0•Updated Sep 19, 2025Sep 19, 2025
haddock-pilot
Public
HADDOCK pilot machinery for running on HPC systems
Shell
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Apache License 2.0
•0•0•0•0•Updated Sep 8, 2025Sep 8, 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
•3•0•0•0•Updated Aug 29, 2025Aug 29, 2025
haddock-restraints-wasm
Public
Rust
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Apache License 2.0
•0•0•0•0•Updated Jul 9, 2025Jul 9, 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•3•5•3•Updated Jun 9, 2025Jun 9, 2025