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@CCPBioSim

CCPBioSim

This is the development repository of the Collaborative Computational Project for Biomolecular Simulation
README.md

CCPBioSim

This GitHub organisation contains software, workshop material and many other types of repositories.

The developer pages at ccpbiosim.github.io describe our development practices and list which repositories are actively maintained. Shared defaults for our repositories, such as dependency update configuration, community-health files and reusable workflows, live in CCPBioSim/.github.

Popular repositories Loading

  1. qmmm-workshop qmmm-workshop Public

    A repository containing the build steps for the ccpbiosim workshop on QM/MM

    Jupyter Notebook 70 21

  2. fesetup fesetup Public archive

    A tool for setting up free energy simulations.

    Python 37 18

  3. CCP5_Simulation_of_BioMolecules CCP5_Simulation_of_BioMolecules Public

    Jupyter Notebook 23 10

  4. mdanalysis-ml-workshop mdanalysis-ml-workshop Public

    Jupyter Notebook 17 5

  5. prepmd prepmd Public

    Automatically prepare structures from the PDB for molecular dynamics simulation

    Python 14 2

  6. biosim-analysis-workshop biosim-analysis-workshop Public

    Workshop on the preparation, execution, and analysis of protein molecular dynamics simulations

    Jupyter Notebook 12 4

Repositories

Showing 10 of 79 repositories
  • SIST Public

    SIST calculates stress-induced structural transition probabilities in superhelical DNA, including strand separation, Z-DNA formation, cruciform extrusion, and competition between these transitions.

    CCPBioSim/SIST's past year of commit activity
    C++ 2 MIT 0 15 2 Updated Nov 1, 2026
  • CodeEntropy Public

    Python package for calculating configurational entropy from molecular dynamics simulations using the multiscale cell correlation method.

    CCPBioSim/CodeEntropy's past year of commit activity
    Python 11 MIT 6 6 2 Updated Oct 31, 2026
  • Python-Template Public template

    A template repository for Python projects within the CCPBioSim organisation

    CCPBioSim/Python-Template's past year of commit activity
    Python 1 MIT 0 1 1 Updated Oct 31, 2026
  • .github Public
    CCPBioSim/.github's past year of commit activity
    1 0 1 1 Updated Oct 31, 2026
  • aiida-gromacs Public

    A GROMACS plugin for AiiDA

    CCPBioSim/aiida-gromacs's past year of commit activity
    Python 8 MIT 7 7 0 Updated Oct 30, 2026
  • aiida-amber Public

    An Amber plugin for AiiDA

    CCPBioSim/aiida-amber's past year of commit activity
    Python 2 MIT 3 5 0 Updated Oct 30, 2026
  • dna-workshop Public
    CCPBioSim/dna-workshop's past year of commit activity
    Jupyter Notebook 1 MIT 0 2 0 Updated Oct 30, 2026
  • protein-preparation-workshop Public

    Preparing protein (only) systems for MD simulation using Ambertools (plus CBAtools)

    CCPBioSim/protein-preparation-workshop's past year of commit activity
    Jupyter Notebook 1 MIT 2 1 0 Updated Oct 30, 2026
  • docking-workflow Public

    A repository containing the build steps for the ccpbiosim workshop on docking

    CCPBioSim/docking-workflow's past year of commit activity
    Jupyter Notebook 6 MIT 0 1 0 Updated Oct 30, 2026
  • openff-workshop Public Forked from openforcefield/ccpbiosim-workshop

    Materials for the workshop during the 2026 CCPBioSim Training Week

    CCPBioSim/openff-workshop's past year of commit activity
    Jupyter Notebook 3 MIT 5 2 0 Updated Oct 30, 2026
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