HADDOCK

All

62 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
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MIT License
•21•13•1•4•Updated Dec 11, 2024Dec 11, 2024
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
•40•119•13•10•Updated Dec 11, 2024Dec 11, 2024
fandas
Public
Repository of the FANDAS code for prediction ssNMR spectra from structure
proteins python3 software nmr chemical-shifts utrecht-university solid-state-nmr spetroscopy
Python
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Apache License 2.0
•0•2•5•2•Updated Dec 9, 2024Dec 9, 2024
haddock-restraints
Public
Generate restraints to be used in HADDOCK
structural-biology haddock tbl restraints
Rust
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MIT License
•1•2•0•1•Updated Dec 9, 2024Dec 9, 2024
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
•1•3•0•0•Updated Dec 9, 2024Dec 9, 2024
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•28•4•5•Updated Dec 5, 2024Dec 5, 2024
protein-glycans
Public
Python
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Apache License 2.0
•0•3•0•0•Updated Dec 4, 2024Dec 4, 2024
cport
Public
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 Dec 2, 2024Dec 2, 2024
.github
Public
0•0•0•0•Updated Nov 28, 2024Nov 28, 2024
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
•7•20•4•0•Updated Nov 19, 2024Nov 19, 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
•4•15•1•0•Updated Oct 14, 2024Oct 14, 2024
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
•27•113•0•0•Updated Oct 14, 2024Oct 14, 2024
proABC-2
Public
Deep learning framework to predict antibody paratope residues
Python
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Apache License 2.0
•2•2•1•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
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
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Apache License 2.0
•114•391•15•7•Updated Sep 3, 2024Sep 3, 2024
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
•17•48•2•0•Updated Sep 2, 2024Sep 2, 2024
cyclic-peptides
Public
Cyclic-peptide - protein complexes benchmark and associated scripts and data
bioinformatics proteins modelling docking structural-bioinformatics utrecht-university cyclic-peptides
Shell
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Apache License 2.0
•2•7•0•0•Updated Aug 31, 2024Aug 31, 2024
ai-antibodies
Public
Jupyter Notebook
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Apache License 2.0
•2•4•0•0•Updated Jul 31, 2024Jul 31, 2024
DeepRank-GNN-esm
Public
Graph Network for protein-protein interface including language model features
Python
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Apache License 2.0
•10•10•1•0•Updated Jul 24, 2024Jul 24, 2024
whiscy
Public
Bioinformatic tool to predict structural protein-protein interfaces
bioinformatics protein-structure sequence-alignment protein-protein-interaction utrecht-university
R
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Apache License 2.0
•2•3•1•0•Updated Jun 27, 2024Jun 27, 2024
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•7•0•0•Updated Apr 30, 2024Apr 30, 2024
disvis
Public
Visualisation of conformational space restriction by distance restraints
Python
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Apache License 2.0
•10•10•8•0•Updated Mar 19, 2024Mar 19, 2024
molmod-data
Public
Data files for the molecular modelling course
Python
•11•12•0•0•Updated Jan 26, 2024Jan 26, 2024
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
•9•22•0•0•Updated Jan 2, 2024Jan 2, 2024
cport-data
Public
Python
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Apache License 2.0
•0•0•0•0•Updated Aug 31, 2023Aug 31, 2023
haddock24-protocol
Public
Data for performing HADDOCK2.4 protocols
bioinformatics proteins modelling docking haddock complexes utrecht-university integrative-modelling
Apache License 2.0
•0•1•0•0•Updated Aug 16, 2023Aug 16, 2023
haddock-mmcif
Public
Encode information from a HADDOCK run to a cif file to be deposited in PDB-Dev.
pdb mmcif haddock utrecht-university pdb-dev
Python
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Apache License 2.0
•0•3•0•0•Updated Jun 28, 2023Jun 28, 2023
contact-filtering
Public
DisVis-based filtering of contacts from co-evolution data (or other sources)
Shell
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Apache License 2.0
•0•1•0•0•Updated Mar 28, 2023Mar 28, 2023
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•12•0•0•Updated Jan 11, 2023Jan 11, 2023
RNA-Pol-III-2022
Public
Data for the RNA-Pol-III tutorial from bonvinlab.org
Apache License 2.0
•0•0•0•0•Updated Oct 11, 2022Oct 11, 2022