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@CDDLeiden Computational Drug Discovery Leiden

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    36 repositories

    • Capricho

      Public
      A Python package to flexibly aggregate ChEMBL data into ML-ready datasets using configurable quality filters
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 17, 2026Mar 17, 2026

    • 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
      •
      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-learningdeep-learningcheminformatics
      reinforcement-learningdeep-learningcheminformaticsdrug-discoveryde-novo-drug-design
      Jupyter Notebook
      •
      MIT License
      •29•180•3•3•Updated Feb 19, 2026Feb 19, 2026

    • uqdd

      Public
      Hybrid Uncertainty Quantification for Bioactivity Assessment
      ensemblehybriduncertainty-quantification
      ensemblehybriduncertainty-quantificationuncertainty-estimationmonte-carlo-dropoutevidential-deep-learningproteochemometricsbioactivitybioactivity-prediction
      Python
      •
      MIT License
      •0•3•0•0•Updated Jan 22, 2026Jan 22, 2026

    • PyTEA-O

      Public
      Python
      •
      MIT License
      •0•1•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
      •
      Creative Commons Attribution 4.0 International
      •224•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • QSPRpred

      Public
      A tool for creating Quantitative Structure Property/Activity Relationship (QSPR/QSAR) models.
      machine-learningcheminformaticsdrug-discovery
      machine-learningcheminformaticsdrug-discoveryqsarqspr
      Jupyter Notebook
      •
      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
      •
      MIT License
      •1•0•0•0•Updated Sep 16, 2025Sep 16, 2025

    • PyVADesign

      Public
      Jupyter Notebook
      •
      Other
      •1•7•0•0•Updated Jul 11, 2025Jul 11, 2025

    • AssayCTX

      Public
      Python
      •
      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.
      cheminformaticsdrug-discoveryalphafold
      cheminformaticsdrug-discoveryalphafoldde-novo-drug-designproteochemometricschemical-language-modelsprotein-language-models
      Jupyter Notebook
      •
      MIT License
      •8•76•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
      •
      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
      •
      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
      •7•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
      •
      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
      •
      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
      •
      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
      •
      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
      •
      MIT License
      •3•0•0•0•Updated Apr 20, 2023Apr 20, 2023
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