DeepRank

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19 repositories

deeprank2
Public
An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.
deep-learning structural-biology pytorch convolutional-neural-networks graph-neural-networks protein-protein-interfaces single-residue-variants
Python
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Apache License 2.0
•10•41•24•3•Updated Dec 18, 2024Dec 18, 2024
3D-Vac
Public
Personalized cancer vaccine design through 3D modelling boosted geometric learning.
Jupyter Notebook
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Apache License 2.0
•0•3•6•0•Updated Dec 3, 2024Dec 3, 2024
h5xplorer
Public
A customizable HDF5 browser with iPython console embbeded
Python
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Apache License 2.0
•2•5•1•1•Updated Sep 3, 2024Sep 3, 2024
DeepRank-GNN-esm
Public
Graph Network for protein-protein interface including language model features
deep-learning scoring language-model protein-protein-interaction utrecht-university graph-networks interface-classification
Python
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Apache License 2.0
•10•26•0•0•Updated Mar 26, 2024Mar 26, 2024
Deeprank-GNN
Public archive
Graph Network for protein-protein interface
graph scoring protein pssm utrecht-university graph-networks protein-protein-interactions interface-classification
Python
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Apache License 2.0
•32•117•3•0•Updated Mar 22, 2024Mar 22, 2024
staged-recipes
Public
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
Python
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BSD 3-Clause "New" or "Revised" License
•5k•0•0•0•Updated Mar 6, 2024Mar 6, 2024
pdbprep
Public
preprocess PDB files for deeprankcore
Python
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Apache License 2.0
•1•4•4•1•Updated Feb 5, 2024Feb 5, 2024
DeepRank-Mut
Public archive
Deep learning framework to predict functional effects of missense variants in human
protein-structure missense-mutations 3dcnn variant-effect-prediction
Python
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Apache License 2.0
•0•1•4•3•Updated Jan 26, 2024Jan 26, 2024
deeprank
Public archive
This repository has been integrated in https://github.com/DeepRank/deeprank2
pytorch docking protein-protein-interaction 3d-cnn
Python
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Apache License 2.0
•26•147•74•0•Updated Nov 28, 2023Nov 28, 2023
pdb2sql
Public
Fast and versatile biomolecular structure PDB file parser using SQL queries
Python
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Apache License 2.0
•12•24•7•0•Updated Mar 17, 2023Mar 17, 2023
pdb2sql_benchmark
Public
Python
•0•0•0•0•Updated Oct 3, 2022Oct 3, 2022
haddock-tools
Public
Set of useful HADDOCK utility scripts
Python
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Apache License 2.0
•17•0•0•0•Updated Jul 14, 2022Jul 14, 2022
PSSMGen
Public
Generates consistent PSSM and/or PDB files for protein-protein complexes
Python
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Apache License 2.0
•5•18•0•0•Updated Jun 26, 2022Jun 26, 2022
iScore
Public
iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines
Python
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Apache License 2.0
•11•27•11•1•Updated Jun 25, 2022Jun 25, 2022
scrapePDB
Public
HTML
•0•0•0•0•Updated Sep 13, 2021Sep 13, 2021
PoNDeR
Public
PointNet for Deep Rank: protein-protein interaction scoring using neural networks
deep-learning pdb point-cloud protein-protein-interaction structural-bioinformatics pointnet
Python
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Apache License 2.0
•1•9•1•0•Updated May 27, 2020May 27, 2020
DeepXplorer
Public
Data browser for HDF5 files generated by DeepRank
Python
•0•3•0•0•Updated Mar 25, 2020Mar 25, 2020
pypdb
Public
A Python API for the RCSB Protein Data Bank (PDB)
Python
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MIT License
•76•0•0•0•Updated Aug 6, 2018Aug 6, 2018
graphRank
Public
graph approach of ranking
Python
•1•0•0•0•Updated Jun 1, 2018Jun 1, 2018