FEP+ Glossary

edge

A line on the perturbation graph drawn between two nodes, representing the perturbation of the ligands represented by the nodes into each other. Also called a "connection".

node

A vertex on the perturbation graph, representing a particular ligand bound to the receptor.

representative structure

A structure that represents the protein-ligand system at one end of an edge of the FEP graph. The representative structure is determined by clustering the simulation frames of the λ=0 window, based on the ligand-protein interactions, and extracting the centroid of the largest cluster.Thus, the representative structure is a frame that displays the most commonly established interactions during the simulation. As replica exchange is used in all of the lambda windows, the trajectory for the λ=0 window is different for different edges ending at the same node, and so the representative structures for that node are different. There are two representative structures for an edge, one for the node at each end, so they are for different ligands. For a node, there is one representative structure for each edge attached to that node, for the ligand represented by that node, so they are for the same ligand.