Pylipid: A Python Toolkit for Analysis of Lipid-Protein Interactions from MD Simulations

The specific interaction of lipids with membrane proteins has gained much attention due to their modulatory effects on protein dynamics and function. Molecular simulations systems allow us predict binding locations, thermodynamics kinetics lipid-protein interactions, complementing relatively sparse experimental data. However, defining interactions lipid sites can be non-trivial. To this end, we have developed an open source python toolkit PyLipID (https://github.com/wlsong/PyLipID) that provides rigorous efficient algorithms for the characterization these interactions. uses a community analysis site detection calculates residence times both residues detected sites. assist structural analysis, generates representative bound poses from simulation data, using scoring function based probability densities. also manuscript-ready figures was designed primarily but is applicable other ligand events.