CHARMM-GUI Membrane Builder publication by Im et al. featured as cover image for Journal of Computational Chemistry
Dr. Wonpil Im
, University of Kansas
One of the ongoing projects in the laboratory of Wonpil Im (University of Kansas and MPSDC team member) has been to contribute to the development of CHARMM-GUI and CHARMM-GUI modules, such as the Ligand Binder and the Membrane Builder. These tools help users generate a series of CHARMM inputs towards a specific purpose, like calculating a protein/ligand binding free energy or building a protein/membrane complex for molecular dynamics simulations. The Consortium’s Computational Modeling Core has provided partial support for the completion of such modules.
Im and his team recently published a paper about the Membrane Builder module in Journal of Computational Chemistry, titled “CHARMM-GUI Membrane Builder toward realistic biological membrane simulations” (reference below). This publication was featured as the cover image for the issue, which can be viewed below. J Comput Chem attached the following note about the article’s relevance:
“On page 1997 (DOI: 10.1002/jcc.23712), Emilia L. Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C. Song, Eder M. Dávila‐Contreras, Yifei Qi, Jumin Lee, Viviana Monje‐Galvan, Richard M. Venable, Jeffery B. Klauda, and Wonpil Im report on the CHARMM‐GUI Membrane Builder, a web‐based user interface designed to interactively build all‐atom protein/membrane or membrane‐only systems for molecular dynamics simulation through an automated optimized process. The cover image illustrates the building process of a protein/membrane system by reading the protein structure, generating pore water/bilayer/bulk water/ions, and combining all the components. ”
(Click to enlarge)
Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem. 2014 Oct 15;35(27):1997-2004. PMID: 25130509. PMCID: PMC4165794 [Available on 2015/10/15].