elelab / lc3b_cancer_paper Goto Github PK

Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark

Repository associated to the publication:

The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer Aykac Fas B, Maiani E, Sora V, Kumar M, Mashkoor M, Lambrughi M, Tiberti M, Papaleo E*, Autophagy, in press, DOI: 10.1080/15548627.2020.1847443

contacts for repository:elenap-at-cancer.dk

The repository contains the input data for modeling and simulations, outputs from analyses and associated scripts to reproduce our data. The the MD trajectories, mutatex and rosetta scans have been deposited in OSF due to space limitation. They can be downloaded from here:

https://osf.io/4zxym/

In simulations_analysis folders with filtered tpr or xtc files do not contain the outputs due to space limitation. Everything is reproducible through the scripts.

A more detailed README file is in each subfolder

1. pdbs/ -> preprocessing and cleaning steps for the PDB files
2. simulations_analysis -> all the analyses done on free and membrane-bound simulations
3. cancermutations -> aggregated analyses of mutations of LC3B/A/C and GABARAP found in cancer samples
4. coevolution -> all the analyses done with gremlin webserver
5. mutatex -> foldx scans a saturation for free protein or complexes

Please cite our publication if you use the material in this repository

Software versions: rosetta 3.11, gromacs 5, foldx-suite5