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.

IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Bioinformatics advances Pub Date : 2025-06-16 eCollection Date: 2025-01-01 DOI:10.1093/bioadv/vbaf129

Gabriel Tiago Galdino, Thomas DesCôteaux, Natalia Teruel, Rafael Najmanovich

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引用次数: 0

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 Additionally, we benchmark a newer version of the Elastic Network Contact Model (ENCoM) for normal mode analysis method, utilizing the same 40 atom-type pairwise interaction matrix that is used in all other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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NRGSuite-Qt：一个PyMOL插件，用于高通量虚拟筛选、分子对接、正常模式分析、分子相互作用研究和结合位点相似性检测。

摘要：我们介绍了一个PyMOL插件NRGSuite-Qt，它为大分子空腔检测、虚拟筛选、小分子对接、正常模式分析、分子相互作用分析和结合位点相似性检测提供了一个全面的工具包。这个完全重新设计的原始NRGSuite（仅限于腔检测和小分子对接）集成了五个新功能：使用Surfaces进行蛋白质-蛋白质和蛋白质-配体相互作用分析，使用NRGRank进行超大质量虚拟筛选，使用IsoMIF进行结合位点相似性检测，使用NRGTEN进行正常模式分析，以及通过与Modeler Suite集成进行突变研究。通过将这些先进的工具合并到一个内聚的平台中，NRGSuite-Qt简化了可视化，并在单个界面内简化了复杂的工作流程。此外，我们对弹性网络接触模型（ENCoM）的新版本进行了基准测试，用于正常模式分析方法，利用所有其他软件中使用的相同的40原子型配对交互矩阵。此版本在多个基准测试中优于默认模型。可用性和实现：安装指南和教程可在https://nrg-qt.readthedocs.io/en/latest/index.html上获得。NRGSuite-Qt用Python实现。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Bioinformatics advances

CiteScore

1.60

自引率

0.00%

发文量