CHARMM-GUI 10 Years for Biomolecular Modeling and Simulation

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare complex molecular simulation systems and input files (CHARMM, NAMD, GROMACS, AMBER, OpenMM, CHARMM/OpenMM) to facilitate the usage of common and advanced simulation techniques. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations: PDB Reader & Manipulator for reading PDB structure files and modifying side chains (e.g., mutation, phosphorylation, protonation, lipid-tail linkers, spin labels, fluorophores, and unnatural amino acids), Glycan Reader for preparation of simulation systems containing carbohydrates or glycoproteins, Quick MD Simulator for solution simulation system generation, Membrane Builder for bilayer simulation system generation, HMMM Builder for HMMM-based bilayer system generation, Monolayer Builder for monolayer simulation system generation, Micelle Builder for micelle simulation system generation, PACE CG Builder for coarse-grained simulation system preparation using the PACE force field. Martini Maker for coarse-grained simulation system preparation using the Martini force field, PBEQ-Solver for electrostatic potential visualization, Ligand Binder for free energy perturbation molecular dynamics simulations for protein-ligand binding affinity calculations, Drude Prepper for conversion of CHARMM additive FF-based systems to Drude polarizable FF-based systems, and GCMC/BD ion simulator for Brownian dynamics of ions across ion channels. Recently, new modules have been integrated into CHARMM-GUI, such as Ligand Reader & Modeler for generation of the CHARMM-compatible topology and parameter files of ligands, Glycolipid Modeler for generation of various glycolipid structures, LPS Modeler for generation of various lipopolysaccharide structures. These new features together with existing modules are expected to be useful in advanced biomolecular modeling and simulation.