When calculating contact-based parameters to measure lipid-protein interactions we are, in effect, averaging over the simulation time and different lipid species
to arrive at a single number. Regardless of how sofisticated the metric we use is, we are still giving up on a lot of information. To overcome this
problem, ProLint takes the calculated metrics and sorts them based on their preferential interaction and for the best scoring residue/lipid combination, it
calculates the distances over time.
Because many systems contain multiple copies of the same protein, and we are usually interested to know how the same residue interacting with the same lipid fares on all copies, ProLint calculates and shows the same distances for all copies in the system. If a selection of protein/residue/lipid does not show a specific binding of the lipid, that is the reason why.
Please note that for efficiency reasons, when calcualting distances, we select the backbone atom/bead of the residue as a reference and one atom/bead from the lipid as a reference (usually one of the headgroup atoms). So, a binding at 1 nm, for example, does not imply that it is better than a binding at 0.5 nm.
No amount of analysis can substitute for visualizing the trajectory. ProLint accelerates research by revealing which residues are interacting with which lipids and by quantifying that interaction in meaningful and physically-grounded ways.
For more information, please see the Visualization Reference on the documenation pages.