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

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Abstract
Summary: We introduce NRGSuite-Qt, a PyMOL plugin, that provides a comprehensive toolkit for macromolecular cavity detection, virtual screening, small-molecule docking, normal mode analysis, analyses of molecular interactions, and detection of binding-site similarities. This complete redesign of the original NRGSuite (restricted to cavity detection and small-molecule docking) 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 Modeler Suite. By merging these advanced tools into a cohesive platform, NRGSuite-Qt simplifies visualization and streamlines complex workflows within a single interface. Additionally, we benchmark a newer version of the Elastic Network Contact Model (ENCoM) for normal mode analysis method, utilizing the same 40 atom-type pairwise interaction matrix that is used in all other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. Avalilability and implementation: The Installation guide and tutorial is available at https://nrg-qt.readthedocs.io/en/latest/index.html. The NRGSuite-Qt is implement in Python.
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