CHARMM‐GUI: A web‐based graphical user interface for CHARMM

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LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands (2017, background): “Among them the CGenFF (18,19), MATCH (20), CHARMM-GUI (21) and CHARMMing (22) servers provide files formatted for CHARMM”
In silico methods and tools for drug discovery (2021, methodology): “Several popular packages for MM/QM simulations include Gromacs [209], NAMD [210], AMBER [189], and CHARMM [190].”
A structural model of the active ribosome-bound membrane protein insertase YidC (2014, methodology): “The YidC model was inserted into the membrane, solvated, and ionized using the Membrane Builder tools on CHARMM-GUI (Jo et al., 2008).”
Computer-Aided Drug Design Methods (2017, methodology): “A convenient web-based tool to perform a number of the steps below is the CHARMM-GUI at www.charmm-gui.org (62).”
CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. (2009, background): “org) (17) that is a superset of a GUI for the biomolecular simulation program CHARMM (18).”
Exploring the free-energy landscape of GPCR activation (2018, methodology): “The structural models were constructed using a combination of VMD plugins (64), the CHARMM-GUI server (65), and MODELER (66).”