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bioRxiv · 10.1101/2025.01.23.634566

NRGSuite-Qt: A PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions and the detection of binding-site similarities

Galdino, G. T.·DesCoteaux, T.·Teruel, N.·Najmanovich, R.
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Abstract

SummaryWe 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 Additionally, we benchmark a newer version of the Elastic Network Contact Model for normal mode analysis method ENCoM, utilizing the same 40 atom-type pairwise interaction matrix that is used in all other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. AvailabilityThe Installation guide and tutorial is available at https://nrg-qt.readthedocs.io/ Contactrafael.najmanovich@umontreal.ca

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Galdino, G. T., DesCoteaux, T., Teruel, N., Najmanovich, R.. 2025-01-24. NRGSuite-Qt: A PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions and the detection of binding-site similarities. https://doi.org/10.1101/2025.01.23.634566

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