PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations
2021
Lipids play important modulatory and structural roles for membrane proteins. Molecular
dynamics simulations are frequently used to provide insights into the nature of these proteinlipid interactions. Systematic comparative analysis requires tools that provide algorithms for
objective assessment of such interactions. We introduce PyLipID, a python package for the
identification and characterization of specific lipid interactions and binding sites on membrane
proteins from molecular dynamics simulations. PyLipID uses a community analysis approach
for binding site detection, calculating lipid residence times for both the individual protein
residues and the detected binding sites. To assist structural analysis, PyLipID produces
representative bound lipid poses from simulation data, using a density-based scoring function.
To estimate residue contacts robustly, PyLipID uses a dual-cutoff scheme to differentiate
between lipid conformational rearrangements whilst bound from full dissociation events. In
addition to the characterization of protein-lipid interactions, PyLipID is applicable to analysis
of the interactions of membrane proteins with other ligands. By combining automated analysis,
efficient algorithms, and open-source distribution, PyLipID facilitates the systematic analysis
of lipid interactions from large simulation datasets of multiple species of membrane proteins.
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