2011
DOI: 10.1021/ci1003619
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CELLmicrocosmos 2.2 MembraneEditor: A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems

Abstract: New perspectives have been developed to understand the processes of modeling heterogeneous membranes. These are crucial steps prior to applying advanced techniques like molecular dynamic simulations of whole membrane systems. Lipid, protein, and membrane packing problems are addressed based on biochemical properties in combination with computational optimization techniques. The CELLmicrocosmos 2.2 MembraneEditor (CmME) is introduced as an appropriate framework to handle such problems by offering diverse algori… Show more

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Cited by 58 publications
(51 citation statements)
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“…The membrane builder from the CHARMM-GUI project can be used to construct membranes with lipids available in the CHARMM force field [53]. Other tools to build membranes A C C E P T E D M A N U S C R I P T 12 using lipids with different force fields are available [37,[54][55][56][57]. PACKMOL is an easy to use and flexible tool for building initial configurations of various systems [58].…”
Section: Initial Configurationsmentioning
confidence: 99%
“…The membrane builder from the CHARMM-GUI project can be used to construct membranes with lipids available in the CHARMM force field [53]. Other tools to build membranes A C C E P T E D M A N U S C R I P T 12 using lipids with different force fields are available [37,[54][55][56][57]. PACKMOL is an easy to use and flexible tool for building initial configurations of various systems [58].…”
Section: Initial Configurationsmentioning
confidence: 99%
“…The initial bilayer system consisting of 512 lipid molecules, 256 per layer, was built with the CELLmicrocosmos MembraneEditor 2.2 (Bielefeld University, Bielefeld, Germany). 34 For the simulation start systems, one copy of the protein model was placed in proximity to the preequilibrated membrane, the simulation box was filled with water, and neutralized with Na þ ions. The orientation of the protein model was slightly altered for different simulation starts, generating seven different starting orientations, whereof in two cases, the 20 N-terminal residues were positioned as transmembrane section.…”
Section: Molecular Dynamics Simulationsmentioning
confidence: 99%
“…Because realistic biological membranes are very heterogeneous structures, special tools are required enabling the generation of these highly-specific structures. The CELLmicrocosmos 2 MembraneEditor (CmME) is such a tool which is also supporting S3D visualization [43].…”
Section: Stereoscopic Membrane Modeling and Visualizationmentioning
confidence: 99%