title: CHARMM-GUI 10 years for biomolecular modeling and simulation.
abstract: CHARMM-GUI, http://www.charmm-gui.org, 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) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler 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.
authors.affiliation: Leadership Computing Facility, Argonne National Laboratory, 9700 Cass Ave, Argonne, Illinois.
authors.forename: Sunhwan
authors.initials: S
authors.lastname: Jo
authors.affiliation: Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China.
authors.forename: Xi
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania.
authors.forename: Jumin
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania.
authors.forename: Seonghoon
authors.initials: S
authors.lastname: Kim
authors.affiliation: Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania.
authors.forename: Sang-Jun
authors.initials: SJ
authors.lastname: Park
authors.affiliation: Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania.
authors.forename: Dhilon S
authors.initials: DS
authors.lastname: Patel
authors.affiliation: Department of Chemistry, The University of Kansas, Lawrence, Kansas.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Beaven
authors.affiliation: Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania.
authors.forename: Kyu Il
authors.initials: KI
authors.lastname: Lee
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois.
authors.forename: Huan
authors.initials: H
authors.lastname: Rui
authors.affiliation: Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania.
authors.forename: Soohyung
authors.initials: S
authors.lastname: Park
authors.affiliation: Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania.
authors.forename: Hui Sun
authors.initials: HS
authors.lastname: Lee
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois.
authors.forename: Benoît
authors.initials: B
authors.lastname: Roux
authors.affiliation: Department of Pharmaceutical Sciences School of Pharmacy, University of Maryland, Baltimore, Maryland.
authors.forename: Alexander D
authors.initials: AD
authors.lastname: MacKerell
authors.affiliation: Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland College Park, Maryland.
authors.forename: Jeffrey B
authors.initials: JB
authors.lastname: Klauda
authors.affiliation: Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania.
authors.forename: Yifei
authors.initials: Y
authors.lastname: Qi
authors.affiliation: Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania.
authors.forename: Wonpil
authors.initials: W
authors.lastname: Im
mesh_terms: D000818:Animals; D002462:Cell Membrane / Q000737:chemistry*; D003196:Computer Graphics; D030562:Databases, Protein; D004578:Electron Spin Resonance Spectroscopy; D006001:Glycoconjugates / Q000737:chemistry*; D006090:Gram-Negative Bacteria / Q000737:chemistry; D006801:Humans; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D012997:Solvents / Q000737:chemistry; D014584:User-Computer Interface
chemical_list: D006001:Glycoconjugates; D008024:Ligands; D011506:Proteins; D012997:Solvents
keywords: Coarse-grained simulation; Glycan; Membranes; Protein-ligand interactions; mmCIF