Molecular dynamics (MD) can be used to identify important molecular interactions in biomolecular systems and examine how these interactions change over the course of the simulation. To accurately quantify the strength of these interactions, interaction energies between residues can be calculated using correlated electronic structure methods. In this work, we use MDAnalysis for reading the MD data; RDKit and PDBrepair for preparing coordinates, and Psi4 for calculating the interaction energies. Combining several software packages into a single workflow can be challenging. To simplify the workflow, we have created MDSAPT, a python package to manage the entire workflow, including rebuilding residues with the correct charge state to set up the electronic structure calculations.

MDSAPT: A python toolkit for analyzing intermolecular interactions in protein structures

ACS Spring 2022

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