LipidSite lipid binding-site analysis
Documentation

Lipid binding sites from MD simulations

LipidSite is a Python package for analysing lipid-protein interactions from molecular dynamics (MD) simulations of membrane proteins. It is optimised for Martini 3 coarse-grained simulations of GPCRs with built-in support for active and inactive state classification, but also works with other membrane-protein systems and force fields including atomistic.

For more, see the documentation.

Input files

Conditions

Up to 500 MB across all files.

Sequence alignment optional

One aligned FASTA (.fasta) for all proteins.

Choose a FASTA alignment .fasta

Analysis settings

Pick a preset or type a residue name. Up to 12 lipid types.

Force field

Sets which protein atoms are selected.

6.0 Å

Distance from a lipid atom that counts as a contact.

protein atoms name BB SC1 SC2 SC3 SC4 SC5

Bound poses and movies

Advanced options

Binding-site detection

ranked by residence time

ns

shorter events discarded

frames

sliding-window length

frames

advance per window (≤ size)

contact fraction for a core residue

contact fraction for peripheral (< core)

residue overlap to merge events into one site

Heatmap & plot layout

alignment positions per row

residues per row in occupancy plots

max events per site, per system

max events per site, cross-repeat