pylipid 1.4.1

PyLipID - A Python Library For Lipid Interaction Analysis

PyLipID is a python library for analyzing lipid interactions with membrane proteins from Molecular Dynamics Simulations. PyLipID has the following main features, please check out the tutorials for examples and the documentations for the API functionalities:

• Analysis of lipid interactions with protein residues using a couple of metrics.

• Detection of binding sites via calculating community structures in the interactions networks.

• Analysis of lipid interactions with binding sites using a couple of metrics.

• Calculation of lipid koff and residence time for protein residues and binding sites.

• Generation of representative bound poses for binding sites.

• Analysis of bound poses for binding sites via automated clustering scheme.

• Adoption of a dual-cutoff scheme to overcome the ‘cage-rattling’ effect of coarse-grained simulations.

• Generation of manuscript-ready figures for analysis.

PyLipID can be used from Jupyter (former IPython, recommended), or by writing Python scripts. The documentaion and tutorials can be found at pylipid.readthedocs.io.

Installation

To install the PyLipID Python package, you need a few Python package dependencies which is listed in the requirement.txt file.

If these dependencies are not available in their required versions, the installation will fail. We thus recommend using the package installer pip:

pip install pylipid

If you know what you are doing and want to build from the source, the package is also available for download on Github via:

git clone https://github.com/wlsong/PyLipID