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FATSLiM / Fast Analysis Toolbox for Simulations of Lipid Membranes

Extracts physical properties from molecular dynamics (MD) simulations of membranes (with or without interacting proteins). As opposed to existing tools, FATSLiM relies on the calculation of normals to infer the bilayer topology. Without loosing accuracy when performing analysis of flat membranes, this approach makes FATSLiM the first tool available to extract thickness, membrane area or area per lipid (APL) from a MD simulations of distorted bilayers or vesicles. Thanks to an efficiency-driven development, it is fast and consumes a rather low amount of memory.


An homology-based method, which predicts a membrane protein's position within a lipid bilayer. iMembrane is part of Memoir (Membrane protein modelling pipeline). It projects the results of coarse-grained molecular dynamics simulations onto any membrane protein structure or sequence provided by the user. iMembrane is simple to use and is a computational method allowing the rapid prediction of a membrane protein's lipid bilayer insertion. Bilayer insertion data are essential in the accurate structural modelling of membrane proteins or the design of drugs that target them.

GridMAT-MD / Grid based Membrane Analysis Tool for use with Molecular Dynamics

Helps in the analysis of lipid bilayers from molecular dynamics simulations. GridMAT-MD can also account for proteins or small molecules within the headgroups of the lipids, closely approximating their occupied lateral area. GridMAT-MD is capable of fast calculations of membrane thickness and area per lipid headgroup with no installation necessary, making it accessible to any of the major operating systems that provide a Perl interpreter. The resulting contour plots are a convenient way to represent the thickness of a lipid bilayer, and the area per lipid calculations are the most convenient and most rigorous that we believe to be publicly available.

[email protected]

Supports the process of analyzing membrane simulations. The values calculated on the geometric structures can be visualized in a user-friendly interactive environment and, then, plotted and exported to different file types. [email protected] supports complex bilayers with a mix of various lipids and proteins. For the calculation of the projected area per lipid, a modification of the well-known Voronoi approach is presented as well as the presentation of a new approach for including atoms into an existing triangulation. In summary, [email protected] is capable of fast calculations of the area per lipid, the bilayer thickness, and in visualizing these data.


Provides a high-performance of molecular dynamics simulations. Desmond includes protein-ligand complexes, small molecules in mixed solvents, organic solids, and synthetic macromolecular complexes. This tool excels in numerical accuracy, which helps to ensure proper modelling of certain thermodynamic relationships that depend on detailed balance. In addition, Desmond provides a robust framework for the calculation of energies and forces for various force field models and is compatible with those models commonly used in both biomolecular and condensed-matter research.