Repositories list

• CodeEntropy

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

  Python

  •

  MIT License

  •6•8•14•0•Updated Aug 6, 2025Aug 6, 2025

• CCP5_Simulation_of_BioMolecules

  Public
  Jupyter Notebook

  •

  Other

  •5•14•0•0•Updated Jul 29, 2025Jul 29, 2025

• branding

  Public
  Branding across CCPBioSim

  1•0•0•0•Updated Jun 3, 2025Jun 3, 2025

• BioSim-analysis-workshop

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

  clusteringmolecular-dynamicsprotein+ 3classificationdimensionality-reductiondocking-molecular

  Jupyter Notebook

  •

  Other

  •4•5•0•0•Updated May 7, 2025May 7, 2025

• python-and-data-workshop

  Public
  Workshop that goes beyond beginner's python to give Jupyter use, intermediate python and data handling with pandas and matplotlib

  HTML

  •

  MIT License

  •3•6•1•1•Updated Apr 11, 2025Apr 11, 2025

• enhanced-sampling-workshop

  Public
  Jupyter Notebook

  •5•0•0•0•Updated Apr 8, 2025Apr 8, 2025

• basic-statistics-workshop

  Public
  Jupyter Notebook

  •

  MIT License

  •1•3•0•0•Updated Apr 4, 2025Apr 4, 2025

• pca-workshop

  Public
  Jupyter Notebook

  •

  MIT License

  •1•6•0•0•Updated Mar 28, 2025Mar 28, 2025

• docking-workflow

  Public
  Jupyter Notebook

  •

  MIT License

  •0•4•0•0•Updated Feb 15, 2025Feb 15, 2025

• software_workshop

  Public
  Python

  •7•0•0•0•Updated Jan 20, 2025Jan 20, 2025

• clustering-workshop

  Public
  Cluster analysis of MD simulation data using RMSD and PCA methods

  Jupyter Notebook

  •

  MIT License

  •1•9•0•0•Updated Nov 24, 2024Nov 24, 2024

• crossflow-workshop

  Public
  A workshop on building biomolecular simulation workflows with crossflow

  Jupyter Notebook

  •

  MIT License

  •2•0•0•0•Updated Nov 21, 2023Nov 21, 2023

• openff-workshop

  Public
  Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week

  Jupyter Notebook

  •

  MIT License

  •2•0•0•0•Updated Sep 27, 2023Sep 27, 2023

• codeentropy-workshop

  Public
  Jupyter notebooks and data files for a CodeEntropy workshop

  Jupyter Notebook

  •0•0•0•0•Updated Sep 15, 2023Sep 15, 2023

• reduce-propka-workshop

  Public
  Training workshop for Reduce and PropKa

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated May 5, 2023May 5, 2023

• equilibration-workshop

  Public
  A workshop to demonstrate approaches to assessing equilibration in MD simulations

  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Feb 22, 2023Feb 22, 2023

• biosimspace-advanced-simulation

  Public
  A workshop covering advanced biomolecular simulation methods with BioSimSpace.

  HTML

  •1•2•0•0•Updated Jan 31, 2023Jan 31, 2023

• biosimspace-workshop

  Public
  Workshop to introduce and teach the BioSimSpace package

  HTML

  •

  MIT License

  •3•1•0•0•Updated Jan 20, 2023Jan 20, 2023

• chemsh-wrapper4enlighten-plugin

  Public
  Python

  •1•0•0•0•Updated Nov 25, 2022Nov 25, 2022

• BSS_FEP_workshop_2022

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Nov 6, 2022Nov 6, 2022

• fesetup

  Public
  A tool for setting up free energy simulations.

  Python

  •

  GNU General Public License v2.0

  •17•35•11•0•Updated Oct 20, 2022Oct 20, 2022

• oxDNA_tutorial

  Public
  TeX

  •2•1•0•0•Updated Sep 30, 2022Sep 30, 2022

• qmmm-workshop

  Public
  Workshop teaching QMMM using Amber

  Jupyter Notebook

  •

  MIT License

  •23•65•0•0•Updated Aug 26, 2022Aug 26, 2022

• MDAnalysis_ML_workshop

  Public
  Jupyter Notebook

  •

  Other

  •5•15•1•0•Updated Jul 28, 2022Jul 28, 2022

• bio_saturne-meshingtool

  Public
  Python

  •0•0•0•0•Updated Jun 22, 2022Jun 22, 2022

• nemd-workshop

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Sep 3, 2021Sep 3, 2021

• enlighten-chemshell-wrapper

  Public archive
  Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems

  Python

  •

  GNU General Public License v3.0

  •8•0•0•0•Updated Aug 23, 2021Aug 23, 2021

• ubiquitin-analysis-workshop

  Public
  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Dec 14, 2020Dec 14, 2020

• propka-workshop

  Public
  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Sep 17, 2020Sep 17, 2020

• Covid-19

  Public
  Space for sharing input files, structures and simulation setups.

  1•0•0•0•Updated May 4, 2020May 4, 2020