Khelashvili Research Group

Resources

Continuum-Molecular Dynamics (CTMD) software

The CTMDapp software calculates the deformation profiles of the bilayer and the free energy cost of the membrane deformation around multi-segment transmembrane proteins, taking into account the radially non-uniform hydrophobic surface of the protein. For more details, please refer to the following publication: Mondal S, Khelashvili G, Shan J, Andersen OS, Weinstein H. Quantitative modeling of membrane deformations by multihelical membrane proteins: application to G-protein coupled receptors. Biophysical Journal 2011 101:2092-2101 PMID 22067146

Real-space fluctuations (RSF) method to quatify material properties of lipid membranes

The RFS method is a computational approach for quantification of the elastic properties of lipidic assemblies of arbitrary shape and composition (including lipid mixtures) from the analysis of molecular dynamics simulations. The method is applicable to diverse lipid assembly types, ranging from bilayers in the liquid ordered and disordered phases to a study of the inverted hexagonal phase. For more details, please refer to the following publication: Doktorova M, Harries D, Khelashvili G. Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations. Physical Chemistry Chemical Physics 2017, 19:16806-16818 PMID 28627570

Self-assembled lipid cubic phases

Structures of cubic phases of various types of monoolein lipids self-assembled during molecular dynamics simulations performed under different hydration conditions can be downloaded, together with the corresponding Martini force-field parameter files used for these simulations. For more details, please refer to the following publication: Johner N, Mondal S, Morra G, Caffrey M, Weinstein H, Khelashvil G. Protein and Lipid Interactions Driving Molecular Mechanisms of in meso Crystallization. Journal of the American Chemical Society 2014 136(8):3271-84 PMID 24494670