Galdino, G. T.; DesCoteaux, T.; Teruel, N.; Najmanovich, R.

We introduce NRGSuite-Qt, a PyMOL plugin that provides a comprehensive toolkit for protein modeling, virtual screening, normal mode analysis, and binding-site similarity calculations. Building on the original NRGSuite plugin for FlexAID, this updated version integrates five new functionalities: protein-protein and protein-ligand interaction analysis using Surfaces, ultra-massive virtual screening with NRGRank, binding-site similarity detection with IsoMIF, normal mode analysis using NRGTEN, and mutational studies through integration with the Modeller Suite. By merging these advanced tools into a cohesive platform, NRGSuite-Qt streamlines complex workflows and facilitates high-throughput computational studies within a single interface. Additionally, we benchmark a newer version of the Elastic Network Contact Model for normal mode analysis method ENCoM, utilizing the same 40 atom-type pairwise interaction matrix that is used in all other software. This version outperforms the default model in multiple benchmarking tests.