A coarse-grained model for disordered and multi-domain proteins

This repository contains codes, raw data and parameter files that used to reproduce the results in the scientific paper A coarse-grained model for disordered and multi-domain proteins by Fan Cao, Sören von Bülow, Giulio Tesei, Kresten Lindorff-Larsen, DOI: https://onlinelibrary.wiley.com/doi/10.1002/pro.5172 

Layout

data/: raw data used for making figures in the paper;

data/IDPs_MDPsCOM_2.2_0.08_2_validate: proteins simulated by CALVADOS 3 model. The corresponding CG topology files, CG trajectory files and calculated Rg data can be found in separate protein folders. ${protein_name}_first.pdb is the CG topology file, ${protein_name}.dcd is the CG trajectory file. Rg_traj.npy is the calculated Rg array.

paper_multidomainCALVADOS/: figures (pdf format) in the paper;

src/: all codes, starting conformations of multi-doamin proteins and experimental data used to reproduce results contained in the paper;

src/BLOCKING/: tools for assessing convergence of Molecular Dynamics simulations (https://github.com/fpesceKU/BLOCKING);

src/expPREs/: paramagnetic relaxation enhancement (PRE) NMR data for optimization;

src/extract_relax: Initial conformations of multi-domain proteins for simulations;

src/domains.yaml: Domain boundaries of used multi-domain proteins in this study;

src/residues_pub.csv: parameters file containing CALVADOS 1, CALVADOS 2 and CALVADOS 3;

figures.ipynb: jupyter version of plotting;

Python code and Jupyter notebooks are also available on GitHub at https://github.com/KULL-Centre/_2024_Cao_CALVADOSCOM

A demo of CALVADOS 3 Colab is available now. Looking forward to receiving your valuable feedbacks.