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

• Published in: Advances in protein chemistry and structural biology Vol. 96; p. 235
• Main Authors: Jo, Sunhwan, Cheng, Xi, Islam, Shahidul M, Huang, Lei, Rui, Huan, Zhu, Allen, Lee, Hui Sun, Qi, Yifei, Han, Wei, Vanommeslaeghe, Kenno, MacKerell, Jr, Alexander D, Roux, Benoît, Im, Wonpil
• Format: Journal Article
• Language: English
• Published: Netherlands 2014
• Subjects: Animals; Computer Graphics; Humans; Internet; Ligands; Models, Molecular; Molecular Dynamics Simulation; Protein Conformation; Proteins - chemistry; Proteins - metabolism; Software; User-Computer Interface; Ligand force field; Spectroscopic probes; MTS reagent; Spin label; Unnatural amino acid; Double electron electron resonance
• ISSN: 1876-1631; 1876-1631
• DOI: 10.1016/bs.apcsb.2014.06.002

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.