Computational Drug Discovery Leiden

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35 repositories

ema-ai-paper
Public
Code accompanying the manuscript "Artificial Intelligence for Regulatory Evidence: A Systematic Document Analysis of European Medicines Agency Regulatory Advice…
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Feb 26, 2026Feb 26, 2026
combinaut
Public
Jupyter Notebook
•0•1•0•0•Updated Feb 20, 2026Feb 20, 2026
DrugEx
Public
De Novo Drug Design with RNNs and Transformers
reinforcement-learning deep-learning cheminformatics
reinforcement-learning deep-learning cheminformatics drug-discovery de-novo-drug-design
Jupyter Notebook
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MIT License
•27•173•3•3•Updated Feb 19, 2026Feb 19, 2026
uqdd
Public
Hybrid Uncertainty Quantification for Bioactivity Assessment
ensemble hybrid uncertainty-quantification
ensemble hybrid uncertainty-quantification uncertainty-estimation monte-carlo-dropout evidential-deep-learning proteochemometrics bioactivity bioactivity-prediction
Python
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MIT License
•0•3•0•0•Updated Jan 22, 2026Jan 22, 2026
PyTEA-O
Public
Python
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MIT License
•0•0•0•0•Updated Dec 8, 2025Dec 8, 2025
ULLA-Leiden
Public
Jupyter Notebook
•2•2•0•0•Updated Nov 14, 2025Nov 14, 2025
teachopencadd
Public
TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
Jupyter Notebook
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Creative Commons Attribution 4.0 International
•225•0•0•0•Updated Nov 5, 2025Nov 5, 2025
QSPRpred
Public
A tool for creating Quantitative Structure Property/Activity Relationship (QSPR/QSAR) models.
machine-learning cheminformatics drug-discovery
machine-learning cheminformatics drug-discovery qsar qspr
Jupyter Notebook
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MIT License
•17•87•2•2•Updated Oct 23, 2025Oct 23, 2025
CBR_teaching
Public
Jupyter Notebook
•1•0•0•0•Updated Sep 29, 2025Sep 29, 2025
acmdd
Public
Labs for ACMDD
Jupyter Notebook
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MIT License
•1•0•0•0•Updated Sep 16, 2025Sep 16, 2025
PyVADesign
Public
Jupyter Notebook
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Other
•1•7•0•0•Updated Jul 11, 2025Jul 11, 2025
AssayCTX
Public
Python
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MIT License
•1•0•0•0•Updated May 21, 2025May 21, 2025
PCMol
Public
Multi-target de novo molecular generator conditioned on AlphaFold's latent protein embeddings.
cheminformatics drug-discovery alphafold
cheminformatics drug-discovery alphafold de-novo-drug-design proteochemometrics chemical-language-models protein-language-models
Jupyter Notebook
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MIT License
•8•75•1•0•Updated Mar 27, 2025Mar 27, 2025
PK-in-generative-drug-design
Public
Jupyter Notebook
•0•5•0•0•Updated Mar 25, 2025Mar 25, 2025
mol_weld
Public
RDKit implementation to weld molecules with different R-groups
Python
•1•0•0•0•Updated Oct 29, 2024Oct 29, 2024
IMERGE-FEP
Public
To enumerate combinations of R-groups for a molecule pair and prune down to logical options for FEP intermediates.
Jupyter Notebook
•1•4•0•0•Updated Oct 22, 2024Oct 22, 2024
qsp-bench
Public
Example repository for benchmarking of QSAR models with QSPRpred.
Jupyter Notebook
•0•0•0•0•Updated Sep 3, 2024Sep 3, 2024
chembl_variants
Public
Jupyter Notebook
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MIT License
•0•1•0•0•Updated Jul 31, 2024Jul 31, 2024
BOO-2024
Public
A collection of introductory materials for BOO students of 2024
1•2•0•0•Updated Jun 10, 2024Jun 10, 2024
gbmt-splits
Public
A tool to create well-balanced data splits for multi-task learning
Python
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GNU General Public License v3.0
•3•2•0•0•Updated Jun 4, 2024Jun 4, 2024
BOO-2023
Public
A collection of introductory materials for BOO students of 2023
1•0•0•0•Updated Nov 13, 2023Nov 13, 2023
kinase-modelling
Public
Jupyter Notebook
•2•5•0•0•Updated Sep 14, 2023Sep 14, 2023
genui-docker
Public
A repository to build and deploy GenUI docker images. GenUI is a collection of web services for interactive molecular generation, QSAR modelling and chemical sp…
Shell
•6•0•0•0•Updated Sep 4, 2023Sep 4, 2023
genui-gui
Public
GenUI frontend application. It provides a GUI to the GenUI REST API web services.
JavaScript
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MIT License
•11•0•0•0•Updated Sep 4, 2023Sep 4, 2023
genui
Public
The backend services of the GenUI framework. The backend provides the REST API used for molecular generation, QSAR modelling and chemical space visualization.
Python
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Other
•17•0•0•0•Updated Sep 4, 2023Sep 4, 2023
ULLA2023_Workshop-Leiden
Public
ULLA 2023 QSAR modelling workshop
Jupyter Notebook
•0•1•0•0•Updated Jul 4, 2023Jul 4, 2023
3ddpd
Public
A repository to generate 3D dynamic protein descriptors (3DDPDs) from molecular dynamics (MS) simulations for proteochemometric (PCM) modelling
Jupyter Notebook
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MIT License
•1•1•0•0•Updated Jun 12, 2023Jun 12, 2023
papyrus-scaffold-visualizer
Public
Visualization of chemical space for QSPRPred data sets and models.
Python
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MIT License
•5•0•0•0•Updated Jun 9, 2023Jun 9, 2023
BindingType
Public
A python package to annotate Class A GPCR or Kinase binding types
Python
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MIT License
•3•0•0•0•Updated Apr 20, 2023Apr 20, 2023
Papyrus-scripts
Public
Jupyter Notebook
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MIT License
•10•22•0•0•Updated Apr 7, 2023Apr 7, 2023