Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

This data set contains i. input topologies and coordinates for 179 non-modified and post-translationally modified (174 in normal and 87 in stress conditions) yeast protein complexes, ii. scripts and parameters for performing molecular dynamics simulations and binding energy calculation with per-residue decomposition, iii. trajectory snapshots of solvent stripped protein complexes, which can be visualized using the corresponding topology files, iv. RMSD calculations (backbone and entire protein) from the production phase of the MD, and v. pdb of the representative structure of the largest cluster from 100 snapshots of the last 10 ns in each simulation. Additionally, PTMs_map.zip contains a Python script (together with an example) for automated addition of PTMs to protein structures using PyTMs in PyMOL.

Publication year:2021

Accessibility:open

Publisher:Zenodo

License:CC-BY-4.0

Format:pdb, zip

Keywords: Molecular dynamics simulations, Post-translational modifications, Protein interactions, PyMOL