The Flexibility and Stability Test (FAST) is a C++ class library designed in the early 2000’s to execute free energy decomposition and reconstitution operations applied to protein structures. The library has been substantially expanded to include structural bioinformatics tools useful in the analysis of protein dynamics. Motivated to advance FAST by improving modeling aspects on atomic packing and solvation, two new algorithms have been developed and implemented, enabling high throughput nonparametric probability density estimation and spatial characterization of cavity volume in proteins. In two separate studies involving molecular dynamics trajectories, novel methods were developed for the analysis of statistical significance in the dynamics of beta-lactamase mutants. Additionally, the core methodologies developed through these studies have been validated as critical components of the FAST library, which aims to advance the field of computational biology and structural bioinformatics as a next generation simulation software for protein and drug design.