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    67 repositories

    • ccpbiosim.github.io

      Public
      A developer facing web resource with various information and dashboards for the core ccpbiosim dev team
      Python
      •
      MIT License
      •0•2•21•1•Updated Jan 5, 2026Jan 5, 2026

    • Python-Template

      Public template
      A template repository for Python projects within the CCPBioSim organisation
      Python
      •
      MIT License
      •0•1•2•1•Updated Jan 5, 2026Jan 5, 2026

    • docking-workflow

      Public
      A repository containing the build steps for the ccpbiosim workshop on docking
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •0•6•0•0•Updated Jan 5, 2026Jan 5, 2026

    • dna-workshop

      Public
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •0•1•1•0•Updated Jan 5, 2026Jan 5, 2026

    • CodeEntropy

      Public
      Python package for calculating configurational entropy from molecular dynamics simulations using the multiscale cell correlation method.
      software
      Python
      •
      MIT License
      •1•11•12•1•Updated Jan 5, 2026Jan 5, 2026

    • basic-analysis-workshop

      Public
      A repository containing the build steps for the ccpbiosim workshop on basic analysis
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •0•5•0•0•Updated Dec 22, 2025Dec 22, 2025

    • aiida-gpcr-workshop

      Public
      A repository containing the build steps for the PSDI workshop on AiiDA tools for data collection
      workshop-materials
      Dockerfile
      •
      MIT License
      •1•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • clustering-workshop

      Public
      A repository containing the build steps for the ccpbiosim workshop on Clustering.
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •1•10•0•0•Updated Dec 22, 2025Dec 22, 2025

    • equilibration-workshop

      Public
      A repository containing the build steps for the ccpbiosim workshop on Equilibration
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Dec 22, 2025Dec 22, 2025

    • python-workshop

      Public
      A repository containing the build steps for the ccpbiosim workshop on Python
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •3•7•0•0•Updated Dec 22, 2025Dec 22, 2025

    • qmmm-workshop

      Public
      A repository containing the build steps for the ccpbiosim workshop on QM/MM
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •22•68•0•0•Updated Dec 22, 2025Dec 22, 2025

    • basic-statistics-workshop

      Public
      A repository containing the build steps for the ccpbiosim workshop on basic statistics
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •1•4•0•0•Updated Dec 22, 2025Dec 22, 2025

    • pdb2pqr-workshop

      Public
      A repository containing the build steps for the ccpbiosim workshop on PDB2PQR Resources
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Dec 22, 2025Dec 22, 2025

    • structure-validation-uglymol

      Public
      A repo to handle the build pipeline for an uglymol instance for the structure validation workshop
      workshop-materials
      HTML
      •
      MIT License
      •1•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • jupyterhub-base

      Public
      A base container image derived from jupyterhub base containers with some extra utilities installed.
      infrastructuretraining-materials
      Dockerfile
      •
      MIT License
      •1•1•0•1•Updated Dec 22, 2025Dec 22, 2025

    • structure-validation-workshop

      Public
      A repository containing the build steps for the ccpbiosim workshop on Structure Validation
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • ubiquitin-analysis-workshop

      Public
      A repository containing the build steps for the ccpbiosim workshop on Ubiquitin analysis
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Dec 22, 2025Dec 22, 2025

    • aiida-lysozyme-workshop

      Public
      A repository containing the build steps for the PSDI workshop on AiiDA tools for data collection
      workshop-materials
      Dockerfile
      •
      MIT License
      •1•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • pca-workshop

      Public
      A repository containing the build steps for the ccpbiosim workshop on PCA
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •1•7•0•0•Updated Dec 22, 2025Dec 22, 2025

    • protein-preparation-workshop

      Public
      Preparing protein (only) systems for MD simulation using Ambertools (plus CBAtools)
      workshop-materialstraining-week-2025
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • protein-ml-workshop

      Public
      Workshop on application of machine learning methoids to the analysis of MD simulation data
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • protein-simulation-workshop

      Public
      Workshop introducing simple MD simulations of a protein using Amber and OpenMM-based approaches
      workshop-materialstraining-week-2025
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Dec 22, 2025Dec 22, 2025

    • mm-gbsa-workshop

      Public
      MM-GBSA analysis of simulations using OpenMM and ParmEd
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • nemd-workshop

      Public
      A repository containing the build steps for the ccpbiosim workshop on non-equilibrium MD
      workshop-materials
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Dec 22, 2025Dec 22, 2025

    • openff-workshop

      Public
      Materials for the workshop during the 2025 CCPBioSim Training Week
      workshop-materialstraining-week-2025
      Jupyter Notebook
      •
      MIT License
      •4•1•2•1•Updated Dec 22, 2025Dec 22, 2025

    • protein-analysis-workshop

      Public
      Analysis of protein simulations with MDTraj
      workshop-materialstraining-week-2025
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • coarse-graining-workshop

      Public
      Introduction to Coarse Graining with YidC: CCPBioSim Training Week 2025
      workshop-materials
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•1•3•0•Updated Dec 22, 2025Dec 22, 2025

    • aiida-plugin-testenv

      Public
      This repository contains the a base image for building a test environment with python, conda, and mamba installed for use with testing aiida plugins.
      data-toolsdata-infrastructure
      Dockerfile
      •
      MIT License
      •2•1•0•0•Updated Dec 22, 2025Dec 22, 2025

    • aiida-gromacs

      Public
      A GROMACS plugin for AiiDA
      data-sciencedata-tools
      Python
      •
      MIT License
      •4•7•6•2•Updated Dec 12, 2025Dec 12, 2025

    • aiida-amber

      Public
      An Amber plugin for AiiDA
      data-sciencedata-tools
      Python
      •
      MIT License
      •2•1•4•2•Updated Dec 12, 2025Dec 12, 2025