| Literature DB >> 25443960 |
Sunhwan Jo1, Xi Cheng2, Shahidul M Islam1, Lei Huang1, Huan Rui1, Allen Zhu1, Hui Sun Lee2, Yifei Qi2, Wei Han3, Kenno Vanommeslaeghe4, Alexander D MacKerell4, Benoît Roux5, Wonpil Im6.
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.Entities:
Keywords: Double electron electron resonance; Ligand force field; MTS reagent; Spectroscopic probes; Spin label; Unnatural amino acid
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Year: 2014 PMID： 25443960 PMCID： PMC4739825 DOI： 10.1016/bs.apcsb.2014.06.002
Source DB: PubMed Journal: Adv Protein Chem Struct Biol ISSN： 1876-1623 Impact factor: 3.507