Figure 3: Examples of RMSD graphs and binding energy histogram of selected molecules.
From: Structure-Based Virtual Ligand Screening on the XRCC4/DNA Ligase IV Interface
(A) RMSD evolution with time for a stable molecule (#231, blue curve, RMSD score = 3) and for an unstable one (#14103, red curve, RMSD score = 1) over a 10 ns MD simulation and within the clamp domain of the Lig4 C-ter fragment. (B) Compounds selected after docking onto the Lig4 clamp domain were ranked according to binding energy. Black and gray boxes correspond to compounds making or not persistent contacts with the target throughout the MD simulation, respectively.
