CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.

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TitleCHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.
Publication TypeJournal Article
Year of Publication2014
AuthorsJo, S, Cheng, X, Islam, SM, Huang, L, Rui, H, Zhu, A, Lee, HSun, Qi, Y, Han, W, Vanommeslaeghe, K, Mackerell, AD, Roux, B, Im, W
JournalAdv Protein Chem Struct Biol
Volume96
Pagination235-65
Date Published2014
ISSN1876-1631
KeywordsAnimals, Computer Graphics, Humans, Internet, Ligands, Models, Molecular, Molecular Dynamics Simulation, Protein Conformation, Proteins, Software, User-Computer Interface
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.

DOI10.1016/bs.apcsb.2014.06.002
Alternate JournalAdv Protein Chem Struct Biol
PubMed ID25443960
PubMed Central IDPMC4739825
Grant ListR01 GM072558 / GM / NIGMS NIH HHS / United States
R01 GM070855 / GM / NIGMS NIH HHS / United States
GM051501 / GM / NIGMS NIH HHS / United States
U54 GM087519 / GM / NIGMS NIH HHS / United States
GM070855 / GM / NIGMS NIH HHS / United States
R01 GM051501 / GM / NIGMS NIH HHS / United States
R29 GM051501 / GM / NIGMS NIH HHS / United States
U54-GM087519 / GM / NIGMS NIH HHS / United States
GM072558 / GM / NIGMS NIH HHS / United States