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@volkamerlab Volkamer Lab

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    36 repositories

    • volkamerlab_org

      Public
      Hugo website for volkamerlab.org
      CSS
      •11•6•13•0•Updated Sep 27, 2024Sep 27, 2024

    • KinFragLib

      Public
      Kinase-focused fragment library
      Jupyter Notebook
      •
      MIT License
      •14•61•4•1•Updated Sep 27, 2024Sep 27, 2024

    • kinodata-3D-affinity-prediction

      Public
      DL models to test added value of using generated complex data for affinity prediction
      Python
      •
      MIT License
      •4•4•0•3•Updated Sep 27, 2024Sep 27, 2024

    • ratar

      Public
      Read-across the targetome
      Python
      •
      MIT License
      •1•2•8•0•Updated Sep 26, 2024Sep 26, 2024

    • MolDockLab

      Public
      MolDockLab is a data-driven workflow developed to identify the best balanced consensus Structure-Based Virtual Screening (SBVS) workflow for a target of interest.
      virtual-screeningmolecular-dockingsbvsconsensus-docking
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Sep 23, 2024Sep 23, 2024

    • MIMB_cellpainting_tutorial

      Public
      TODO
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Sep 18, 2024Sep 18, 2024

    • ai_in_chemistry_workshop

      Public
      ai_in_chemistry_workshop
      Jupyter Notebook
      •
      MIT License
      •7•58•0•0•Updated Sep 16, 2024Sep 16, 2024

    • Transformers4MPP_review

      Public
      Supplementary information for creating the figures in the review
      Jupyter Notebook
      •
      MIT License
      •1•4•0•0•Updated Aug 23, 2024Aug 23, 2024

    • 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
      •202•755•47•10•Updated Jul 11, 2024Jul 11, 2024

    • kinodata-3D

      Public
      Protein kinase-ligand complex generation using template docking
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Jul 4, 2024Jul 4, 2024

    • CACHE5_public

      Public
      Workflow for the CACHE5 submission of the Volkamer Lab
      Jupyter Notebook
      •0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • DockM8

      Public
      All in one Structure-Based Vitual Screening workflow based on the concept of consensus docking.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • KinaseFocusedFragmentLibrary

      Public
      Subpocket-based fragmentation and recombination of kinase inhibitors
      Python
      •
      MIT License
      •0•7•4•1•Updated May 6, 2024May 6, 2024

    • opencadd

      Public
      A Python library for structural cheminformatics
      Python
      •
      MIT License
      •18•91•28•4•Updated Feb 25, 2024Feb 25, 2024

    • maxsmi

      Public
      maxsmi: a guide to SMILES augmentation. Find the optimal SMILES augmentation for accurate molecular prediction.
      cheminformaticsdata-augmentationdeep-learning
      Jupyter Notebook
      •
      MIT License
      •4•28•5•6•Updated Feb 22, 2024Feb 22, 2024

    • kissim

      Public
      Subpocket-based fingerprint for kinase pocket comparison
      Python
      •
      MIT License
      •4•30•8•1•Updated Sep 24, 2023Sep 24, 2023

    • CADDSeminar_2023

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•4•Updated Jul 13, 2023Jul 13, 2023

    • plipify

      Public
      Jupyter Notebook
      •
      MIT License
      •6•14•7•5•Updated Jan 24, 2023Jan 24, 2023

    • lab_repos_check

      Public
      Check the CI status of the Volkamer Lab's repositories
      MIT License
      •0•2•0•0•Updated Dec 31, 2022Dec 31, 2022

    • kissim_app

      Public
      Kinome-wide structural pocket similarity
      Jupyter Notebook
      •
      MIT License
      •3•10•5•0•Updated Dec 26, 2022Dec 26, 2022

    • cicag_klifs_workshop

      Public
      CICAG workshop on KLIFS, OpenCADD-KLIFS, and KiSSim
      Jupyter Notebook
      •2•1•0•0•Updated Nov 20, 2022Nov 20, 2022

    • kinase_similarity_pipeline_paper

      Public
      Kinase Similarity Assessment Pipeline For Off-Target Prediction
      open-sourcepipelineside-effectskinaselivecomsteachopencadd
      TeX
      •
      Creative Commons Attribution 4.0 International
      •0•0•1•0•Updated Jun 23, 2022Jun 23, 2022

    • toxsmi

      Public
      Toxicity prediction models
      Python
      •
      MIT License
      •15•1•0•0•Updated Feb 17, 2022Feb 17, 2022

    • ai_in_medicine

      Public
      Jupyter Notebook
      •9•32•2•0•Updated Feb 14, 2022Feb 14, 2022

    • OpenCADDSuperpositionBenchmark

      Public
      Benchmarking the OpenCADD superposition methods
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 3, 2022Jan 3, 2022

    • CPrecalibration_manuscript_SI

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Sep 24, 2021Sep 24, 2021

    • TeachOpenCADD-BindingSiteDetection

      Public
      TeachOpenCADD talktorial on binding site detection
      Jupyter Notebook
      •
      MIT License
      •3•4•3•0•Updated Aug 10, 2021Aug 10, 2021

    • DL_in_VS_review

      Public
      Deep learning in virtual screening, a review
      Jupyter Notebook
      •3•4•0•0•Updated Apr 26, 2021Apr 26, 2021

    • cptox21_manuscript_SI

      Public
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Feb 7, 2021Feb 7, 2021

    • knowtox_manuscript_SI

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •4•5•0•0•Updated Jan 5, 2021Jan 5, 2021