Combining MD simulations and scoring methods to computationally model ubiquitylated linker histones in chromatosomes

README

List of public repositories:

Code https://github.com/AG-Peter/H1Ub_in_chromatosomes

Simulations https://sawade.io/H1Ub_in_chromatosomes/

Software versions

Python packages in requirements.txt.

Molsim: Gromacs2016.3 and Gromacs2021.2

Visualization: vmd1.9.3

Isopeptide bond and rotamer generation: UCSF Chimera 1.16

Sketch-map version: https://github.com/lab-cosmo/sketchmap/tree/b7aa957bf3bf764854ce309b98f68e869f080916

Scripts

Interpenetration and scoring algorithm:

Obtain via:

$ git clone https://github.com/AG-Peter/H1Ub_in_chromatosomes.git
cd interpenetration_algorithm
pip install .

List of input files:

input coordinates https://github.com/AG-Peter/H1Ub_in_chromatosomes/tree/main/input_files/starting_conformations

molsim parameters https://github.com/AG-Peter/H1Ub_in_chromatosomes/tree/main/input_files/