SOMMD: an R package for the analysis of molecular dynamics simulations using self-organizing map.

Abstract

Molecular dynamics (MD) simulations provide critical insights into biomolecular processes but they generate complex high-dimensional data that are often difficult to interpret directly. Dimensionality reduction methods like principal component analysis, time-lagged independent component analysis, and self-organizing maps (SOMs) have helped in extracting essential information on functional dynamics. However, there is a growing need for a user-friendly and flexible framework for SOM-based analyses of MD simulations. Such a framework should offer adaptable workflows, customizable options, and direct integration with a widely adopted analysis software. We designed and developed SOMMD, an R package to streamline MD analysis workflows. SOMMD facilitates the interpretation of atomistic trajectories through SOMs, providing tools for each stage of the workflow, from importing a wide range of MD trajectories data types to generating enhanced visualizations. The package also includes three example projects that demonstrate how SOM can be applied in real-world scenarios, including cluster analysis, pathways mapping and transition networks reconstruction. SOMMD is available on CRAN (https://CRAN.R-project.org/package=SOMMD) and on GitHub (https://github.com/alepandini/SOMMD).