Repositories list

• 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 Dec 31, 2025Dec 31, 2025

• 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•15•1•Updated Dec 29, 2025Dec 29, 2025

• 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

• 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 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

• dna-workshop

  Public
  workshop-materials

  Jupyter Notebook

  •

  MIT License

  •0•1•1•0•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

• Python-Template

  Public template
  A template repository for Python projects within the CCPBioSim organisation

  Python

  •

  MIT License

  •0•1•2•0•Updated Dec 11, 2025Dec 11, 2025