CHARMM‐GUI 10 years for biomolecular modeling and simulation

<jats:p>CHARMM‐GUI, <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.charmm-gui.org">http://www.charmm-gui.org</jats:ext-link>, is a web‐based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. 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 set up a broad range of simulations: (1) <jats:italic>PDB Reader & Manipulator</jats:italic>, <jats:italic>Glycan Reader</jats:italic>, and <jats:italic>Ligand Reader & Modeler</jats:italic> for reading and modifying molecules; (2) <jats:italic>Quick MD Simulator</jats:italic>, <jats:italic>Membrane Builder</jats:italic>, <jats:italic>Nanodisc Builder</jats:italic>, <jats:italic>HMMM Builder</jats:italic>, <jats:italic>Monolayer Builder</jats:italic>, <jats:italic>Micelle Builder</jats:italic>, and <jats:italic>Hex Phase Builder</jats:italic> for building all‐atom simulation systems in various environments; (3) <jats:italic>PACE CG Builder</jats:italic> and <jats:italic>Martini Maker</jats:italic> for building coarse‐grained simulation systems; (4) <jats:italic>DEER Facilitator</jats:italic> and <jats:italic>MDFF/xMDFF Utilizer</jats:italic> for experimentally guided simulations; (5) <jats:italic>Implicit Solvent Modeler</jats:italic>, <jats:italic>PBEQ‐Solver</jats:italic>, and <jats:italic>GCMC/BD Ion Simulator</jats:italic> for implicit solvent related calculations; (6) <jats:italic>Ligand Binder</jats:italic> for ligand solvation and binding free energy simulations; and (7) <jats:italic>Drude Prepper</jats:italic> for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM‐GUI, such as <jats:italic>Glycolipid Modeler</jats:italic> for generation of various glycolipid structures, and <jats:italic>LPS Modeler</jats:italic> for generation of lipopolysaccharide structures from various Gram‐negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM‐GUI development project. © 2016 Wiley Periodicals, Inc.</jats:p>