CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations
By E. Wu, Xi Cheng, Sunhwan Jo, H. Rui, Kevin C. Song, Eder M. Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, R. Venable and 2 more. Journal of Computational Chemistry, 2014
2,421 citations recorded by the source corpus.
CHARMM‐GUI Membrane Builder, http://www.charmm‐gui.org/input/membrane, is a web‐based user interface designed to interactively build all‐atom protein/membrane or membrane‐only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance‐based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM‐GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments. © 2014 Wiley Periodicals, Inc.
Subfields: Biomedical Engineering, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/12116ecb4fd700363a8522e025fae3d221316e54
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Citations in the corpus
- CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. (2018, positive): “Since its first release in 2007, CHARMM-GUI Membrane Builder 27–30 , a publicly available web-based tool (http://www.charmm-gui.org/input/membrane), has greatly facilitated the generation of complex membrane systems.”
- Inward-facing conformation of a multidrug resistance MATE family transporter (2019, methodology): “The two PfMATE structures were embedded in lipid bilayers of varying composition using CHARMM-GUI (62).”
- CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates (2019, methodology): “This example illustrates how to build a complete CTB:GM1 pentameric complex using Glycan Reader & Modeler and to insert the ceramide lipid portions into a membrane bilayer using Membrane Builder (Jo et al. 2009; Wu et al. 2014) (Figure 4C); see Section 3 of Supplementary Data for the detailed steps.”