FATSLiM: a fast and robust software to analyze MD simulations of membranes

Summary: When studying biological membranes, Molecular Dynamics (MD) simulations reveal to be quite complementary to experimental techniques. Because the simulated systems keep increasing both in size and complexity, the analysis of MD trajectories need to be computationally efficient while being robust enough to perform analysis on membranes that may be curved or deformed due to their size and/or protein-lipid interactions. This work presents a new software named FATSLiM (‘Fast Analysis Toolbox for Simulations of Lipid Membranes’) that can extract physical properties from MD simulations of membranes (with or without interacting proteins). Because it relies on the calculation of local normals, FATSLiM does not depend of the bilayer morphology and thus can handle with the same accuracy vesicles for instance. Thanks to an efficiency-driven development, it is also fast and consumes a rather low amount of memory.
Availability and Implementation: FATSLiM (http://fatslim.github.io) is a stand-alone software written in Python. Source code is released under the GNU GPLv3 and is freely available at https://github.com/FATSLiM/fatslim. A complete online documentation including instructions for platform-independent installation is available at http://pythonhosted.org/fatslim.
Contact: [e-mail]
Supplementary information: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics - December 28, 2016 Category: Bioinformatics Authors: Buchoux, S. Tags: STRUCTURAL BIOINFORMATICS Source Type: research