Using Machine Learning to Analyze Molecular Dynamics Simulations of Biomolecules

Machine learning (ML) techniques have become powerful tools in both industrial and academic settings. Their ability to facilitate analysis of complex data and generation of predictive insights is transforming how scientific problems are approached across a wide range of disciplines. In this tutorial, we present a cursory introduction to three widely used ML techniques─logistic regression, random forest, and multilayer perceptron─applied toward analyzing molecular dynamics (MD) trajectory data. We employ our chosen ML models to the study of the SARS-CoV-2 spike protein receptor binding domain interacting with the receptor ACE2. We develop a pipeline for processing MD simulation trajectory data and identifying residues that significantly impact the stability of the complex.