https://github.com/kull-centre/colabcalvados

Jupyter Notebook on Google Colaboratory to generate and refine protein conformational ensembles from CALVADOS simulations

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Repository

Jupyter Notebook on Google Colaboratory to generate and refine protein conformational ensembles from CALVADOS simulations

Basic Info

Host: GitHub
Owner: KULL-Centre
License: gpl-3.0
Language: Jupyter Notebook
Default Branch: main
Homepage:
Size: 4.26 MB

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Stars: 3
Watchers: 2
Forks: 0
Open Issues: 0
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Created over 1 year ago · Last pushed 6 months ago

Metadata Files

Readme License

ColabCALVADOS

CUDA module in Colab CALVADOS is unavailable because of a recent update from Google Colab. We are using OpenCL to accelerate simulations for now. --09.09.2025

This repository provides Jupyter Notebooks designed to explore the conformational properties of intrinsically disordered regions (IDRs) and multi-domain proteins (MDPs) through molecular dynamics (MD) simulations on Google Colaboratory. Simulations are performed using CALVADOS, an implicit-solvent coarse-grained model.

Folder Structure

simulate_and_reweight This folder includes the notebook CALVADOS_simulate_and_reweight.ipynb along with instructions for integrating simulations with experimental small-angle X-ray scattering (SAXS) data. The workflow involves applying Bayesian/Maximum-Entropy reweighting to refine the conformational ensemble of the protein of study.
simulate This folder contains a lite version of the notebook, focused on running simulations and backmapping to all-atom resolution.

Getting Started

You will need a Google account and Google Chrome to work with the notebooks.

Browse the Data. Visit the data/SAXS folder to find sequences, PDB structures and SAXS data for several IDRs and MDPs.
- Select a protein and download its PDB (needed only for MDPs) and SAXS data file (.dat).
- Alternatively, you can analyze a protein of your choice by providing your own sequence and SAXS data file.
Access the Notebook. The lab exercise is conducted using a Jupyter Notebook hosted on Google Colab. To access the notebook, click the "Open in Colab" badge below. Further instructions can be found here and here.