Sunhwan Jo, Xi Cheng, S. Islam, Lei Huang, H. Rui, Allen Zhu, Hui-Sun Lee, Yifei Qi, Wei Han, K. Vanommeslaeghe, Alexander D. MacKerell, B. Roux, W. Im
2014.8.24Advances in Protein Chemistry and Structural Biology
tlooto Summary
Functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator are described, such as ligand force field generation, incorporation of methanethiosulfonate spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids to be useful in advanced biomolecular modeling and simulation of proteins.
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 its original development 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 (MTS) 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.
Citation format
JO, Sunhwan, et al. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing non-standard residues. Advances in Protein Chemistry and Structural Biology, 2014, 96: 235–265.