MDAnalysis (http://mdanalysis. org) is a library for structural and temporal analysis of
molecular dynamics (MD) simulation trajectories and individual protein structures. MD …

The success of molecular modeling and computational chemistry efforts are, by definition,
dependent on quality software applications. Open source software development provides …

Lipids play important modulatory and structural roles for membrane proteins. Molecular
dynamics simulations are frequently used to provide insights into the nature of these protein …

Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological
membranes to carry out functions such as cell signalling, enzymatic activity, or membrane …

Generation and analysis of time-series data is relevant to many quantitative fields ranging
from economics to fluid mechanics. In the physical sciences, structures such as metastable …

Recent advances in molecular simulations have allowed scientists to investigate slower
biological processes than ever before. Together with these advances came an explosion of …

The quantitative assessment of uncertainty and sampling quality is essential in molecular
simulation. Many systems of interest are highly complex, often at the edge of current …

The development of reliable and extensible molecular mechanics (MM) force fields—fast,
empirical models characterizing the potential energy surface of molecular systems—is …

The design of compounds that can discriminate between closely related target proteins
remains a central challenge in drug discovery. Specific therapeutics targeting the highly …

Molecular dynamics simulations are now widely used to study emergent phenomena in lipid
membranes with complex compositions. Here, we present LiPyphilic—a fast, fully tested …