lipsite lipid binding-site analysis
Documentation

Membrane-protein MD · lipid–protein interactions

Lipid binding sites from membrane-protein simulations

lipsite computes per-residue lipid occupancy, ranked binding sites with residence times, and representative bound poses from membrane-protein molecular dynamics trajectories.

  1. 1

    Prepare your data

    Correct periodic boundaries and remove solvent, leaving protein and lipids only.

  2. 2

    Add your protein

    Name it, set the residue offset, then drop in the topology and trajectory.

  3. 3

    Set lipids and run

    List the lipid residues to analyse, then start the run.

  4. 4

    Download results

    Save the results link and download every output as a single zip.

Simulation data

Each repeat is one topology (.pdb) plus one trajectory (.xtc). Click a box to choose a file, or drag it in. Add more proteins to analyse them together.

Comparison

Repeats of one condition, under General — the standard analysis.

Up to 5 GB in total per job, across every file.

Sequence alignment optional

One aligned FASTA (.fasta) covering all proteins. Each protein picks its record below, and occupancy is mapped onto the aligned sequence as a heatmap.

Choose a FASTA alignment .fasta
Preparing a trajectory with gmx trjconv

Correct periodic boundaries and write a solvent-free trajectory plus a matching topology frame. Choose a protein + lipids group when trjconv prompts for an output selection.

gmx trjconv -f prod.xtc -s topol.tpr -pbc mol -center -o run.xtc
gmx trjconv -f prod.xtc -s topol.tpr -pbc mol -center -dump 0 -o run.pdb

Analysis settings

Applied to every protein. Only the lipids are required; the rest have sensible defaults.

Add a preset or type your own — up to 12 types, each analysed separately.

Force field

Sets the base protein atom selection.

6.0 Å

Distance from any lipid atom that counts as a contact.

selection name BB SC1 SC2 SC3 SC4 SC5

Advanced options Binding-site detection thresholds and pose extraction — optional, with defaults matching the lipsite CLI.
Binding-site detection

How binding sites and residence times are found by the 3-step sliding-window search over the contact map.

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)

Bound-lipid poses