ColabCALVADOS

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.

1. 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.

2. 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.

   

Authors

Fan Cao (@fancaoErik)

Francesco Pesce (@FrPsc)

Giulio Tesei (@gitesei)

Kresten Lindorff-Larsen (@lindorff-larsen)