title: CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.
abstract: CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since it is originally developed 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 including free energy calculation and large-scale coarse-grained representation. Here, we describe functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator, such as ligand force field generation, incorporation of methanethiosulfonate spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids. These new features are expected to be useful in advanced biomolecular modeling and simulation of proteins.
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, USA.
authors.forename: Sunhwan
authors.initials: S
authors.lastname: Jo
authors.affiliation: Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, USA.
authors.forename: Xi
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, USA.
authors.forename: Shahidul M
authors.initials: SM
authors.lastname: Islam
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Huang
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, USA.
authors.forename: Huan
authors.initials: H
authors.lastname: Rui
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, USA.
authors.forename: Allen
authors.initials: A
authors.lastname: Zhu
authors.affiliation: Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, USA.
authors.forename: Hui Sun
authors.initials: HS
authors.lastname: Lee
authors.affiliation: Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, USA.
authors.forename: Yifei
authors.initials: Y
authors.lastname: Qi
authors.affiliation: Beckman Institute and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Han
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA.
authors.forename: Kenno
authors.initials: K
authors.lastname: Vanommeslaeghe
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA.
authors.forename: Alexander D
authors.initials: AD
authors.lastname: MacKerell
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, USA. Electronic address: roux@uchicago.edu.
authors.forename: Benoît
authors.initials: B
authors.lastname: Roux
authors.affiliation: Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, USA. Electronic address: wonpil@ku.edu.
authors.forename: Wonpil
authors.initials: W
authors.lastname: Im
mesh_terms: D000818:Animals; D003196:Computer Graphics; D006801:Humans; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D011506:Proteins
keywords: Double electron electron resonance; Ligand force field; MTS reagent; Spectroscopic probes; Spin label; Unnatural amino acid