MDAnalysis (http://mdanalysis.org) is a library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. MD simulations of biological molecules have become an important tool to elucidate the relationship between molecular structure and physiological function. Simulations are performed with highly optimized software packages on HPC resources but most codes generate output trajectories in their own formats so that the development of new trajectory analysis algorithms is confined to specific user communities and widespread adoption and further development is delayed. MDAnalysis addresses this problem by abstracting access to the raw simulation data and presenting a uniform object-oriented Python interface to the user. It thus enables users to rapidly write code that is portable and immediately usable in virtually all biomolecular simulation communities. The user interface and modular design work equally well in complex scripted work flows, as foundations for other packages, and for interactive and rapid prototyping work in IPython / Jupyter notebooks, especially together with molecular visualization provided by nglview and time series analysis with pandas. MDAnalysis is written in Python and Cython and uses NumPy arrays for easy interoperability with the wider scientific Python ecosystem. It is widely used and forms the foundation for more specialized biomolecular simulation tools. MDAnalysis is available under the GNU General Public License v2.

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: sebastien.buchoux@u-picardie.frSupplementary information: Supplementary data are available at Bioinformatics online.

Specialized lipid domains (rafts) that are generally enriched in sterols and sphingolipids, are most likely present in cell membranes of animals, plants and fungi. While cholesterol and ergosterol are predominant in vertebrates and fungi, plants possess complex sterol profiles, dominated by sitosterol and stigmasterol in Arabidopsis thaliana. Fully hydrated model membranes of composition approaching those found in rafts of mammals, fungi and plants were investigated by means of solid-state 2H-NMR, using deuterated dipalmitoylphosphatidylcholine (2H(62)-DPPC). The dynamics of such membranes was determined through measuring of membrane ordering or disordering properties. The presence of the liquid-ordered, lo, phase, which may be an indicator of rigid sterol-sphingolipid domains, was detected in all binary or ternary mixtures of all sterols investigated. Of great interest, the dynamics of ternary mixtures mimicking rafts in plants (phytosterol/glucosylcerebroside/DPPC), showed a lesser temperature sensitivity to thermal shocks, on comparing to systems mimicking rafts in mammals and fungi. This effect was particularly marked with sitosterol. The presence of an ethyl group branched on the alkyl chain of sitosterol and stigmasterol is proposed as reinforcing the membrane cohesion by additional attractive van der Waals interactions with the alkyl chains of sphingolipids and phospholipids. As a side result, the elevated resolution of NMR spectra in the presence of sitosterol also suggests domains of smaller size than with other sterols. Finally, the role of phytosterols in maintaining plant membranes in a state of dynamics less sensitive to temperature shocks is discussed.