CCPBioSim

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67 repositories

com_ccpbiosim
Public
A repository containing the source code for the CCPBioSim web component extension to joomla
joomla-component webapp
PHP
•
MIT License
•0•0•0•0•Updated Feb 5, 2026Feb 5, 2026
prepmd
Public
Automatically prepare structures from the PDB for molecular dynamics simulation
software
Python
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GNU Affero General Public License v3.0
•0•2•2•0•Updated Feb 5, 2026Feb 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•8•0•Updated Feb 5, 2026Feb 5, 2026
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•6•1•Updated Feb 2, 2026Feb 2, 2026
aiida-gromacs
Public
A GROMACS plugin for AiiDA
data-science data-tools
Python
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MIT License
•4•8•10•0•Updated Jan 30, 2026Jan 30, 2026
aiida-amber
Public
An Amber plugin for AiiDA
data-science data-tools
Python
•
MIT License
•2•2•7•0•Updated Jan 30, 2026Jan 30, 2026
jupyterhub-base
Public
A base container image derived from jupyterhub base containers with some extra utilities installed.
infrastructure training-materials
Dockerfile
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MIT License
•1•1•0•1•Updated Jan 29, 2026Jan 29, 2026
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 Jan 29, 2026Jan 29, 2026
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-tools data-infrastructure
Dockerfile
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MIT License
•2•1•0•0•Updated Jan 29, 2026Jan 29, 2026
mm-gbsa-workshop
Public
MM-GBSA analysis of simulations using OpenMM and ParmEd
Jupyter Notebook
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MIT License
•0•2•0•0•Updated Jan 29, 2026Jan 29, 2026
openff-workshop
Public
Materials for the workshop during the 2025 CCPBioSim Training Week
workshop-materials training-week-2025
Jupyter Notebook
•
MIT License
•4•1•1•0•Updated Jan 29, 2026Jan 29, 2026
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 Jan 29, 2026Jan 29, 2026
dna-workshop
Public
workshop-materials
Jupyter Notebook
•
MIT License
•0•1•1•0•Updated Jan 29, 2026Jan 29, 2026
nemd-workshop
Public
A repository containing the build steps for the ccpbiosim workshop on non-equilibrium MD
workshop-materials
Jupyter Notebook
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MIT License
•0•2•0•0•Updated Jan 29, 2026Jan 29, 2026
protein-analysis-workshop
Public
Analysis of protein simulations with MDTraj
workshop-materials training-week-2025
Jupyter Notebook
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MIT License
•0•1•0•0•Updated Jan 29, 2026Jan 29, 2026
protein-simulation-workshop
Public
Workshop introducing simple MD simulations of a protein using Amber and OpenMM-based approaches
workshop-materials training-week-2025
Jupyter Notebook
•
MIT License
•0•2•0•0•Updated Jan 29, 2026Jan 29, 2026
protein-preparation-workshop
Public
Preparing protein (only) systems for MD simulation using Ambertools (plus CBAtools)
workshop-materials training-week-2025
Jupyter Notebook
•
MIT License
•0•1•0•0•Updated Jan 29, 2026Jan 29, 2026
docking-workflow
Public
A repository containing the build steps for the ccpbiosim workshop on docking
workshop-materials
Jupyter Notebook
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MIT License
•0•6•0•0•Updated Jan 29, 2026Jan 29, 2026
equilibration-workshop
Public
A repository containing the build steps for the ccpbiosim workshop on Equilibration
workshop-materials
Jupyter Notebook
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MIT License
•0•3•0•0•Updated Jan 29, 2026Jan 29, 2026
python-workshop
Public
A repository containing the build steps for the ccpbiosim workshop on Python
workshop-materials
Jupyter Notebook
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MIT License
•3•7•0•0•Updated Jan 29, 2026Jan 29, 2026
aiida-lysozyme-workshop
Public
A repository containing the build steps for the PSDI workshop on AiiDA tools for data collection
workshop-materials
Dockerfile
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MIT License
•1•1•0•0•Updated Jan 29, 2026Jan 29, 2026
pca-workshop
Public
A repository containing the build steps for the ccpbiosim workshop on PCA
workshop-materials
Jupyter Notebook
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MIT License
•1•7•0•0•Updated Jan 29, 2026Jan 29, 2026
clustering-workshop
Public
A repository containing the build steps for the ccpbiosim workshop on Clustering.
workshop-materials
Jupyter Notebook
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MIT License
•1•10•0•0•Updated Jan 29, 2026Jan 29, 2026
aiida-gpcr-workshop
Public
A repository containing the build steps for the PSDI workshop on AiiDA tools for data collection
workshop-materials
Dockerfile
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MIT License
•1•1•0•0•Updated Jan 29, 2026Jan 29, 2026
pdb2pqr-workshop
Public
A repository containing the build steps for the ccpbiosim workshop on PDB2PQR Resources
workshop-materials
Jupyter Notebook
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MIT License
•0•2•0•0•Updated Jan 29, 2026Jan 29, 2026
ubiquitin-analysis-workshop
Public
A repository containing the build steps for the ccpbiosim workshop on Ubiquitin analysis
workshop-materials
Jupyter Notebook
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MIT License
•0•2•0•0•Updated Jan 29, 2026Jan 29, 2026
structure-validation-workshop
Public
A repository containing the build steps for the ccpbiosim workshop on Structure Validation
workshop-materials
Jupyter Notebook
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MIT License
•1•1•0•0•Updated Jan 29, 2026Jan 29, 2026
basic-analysis-workshop
Public
A repository containing the build steps for the ccpbiosim workshop on basic analysis
workshop-materials
Jupyter Notebook
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MIT License
•0•5•0•0•Updated Jan 29, 2026Jan 29, 2026
structure-validation-uglymol
Public
A repo to handle the build pipeline for an uglymol instance for the structure validation workshop
workshop-materials
HTML
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MIT License
•1•1•0•0•Updated Jan 29, 2026Jan 29, 2026
basic-statistics-workshop
Public
A repository containing the build steps for the ccpbiosim workshop on basic statistics
workshop-materials
Jupyter Notebook
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MIT License
•1•4•0•0•Updated Jan 29, 2026Jan 29, 2026