Figure 2: Virtual screening on the Lig4 clamp domain.
From: Structure-Based Virtual Ligand Screening on the XRCC4/DNA Ligase IV Interface
(A) Overlap of the eleven MD simulation-extracted structures of Lig4 clamp domain used for molecular docking. (B) Example of clustering analysis within a Lig4 clamp structure after docking, showing molecule #93291 with the superimposition of ten conformers in a single position cluster. The clamp structure is represented in surface with persistent contact colored as in Fig. 1C. (C) Example of a lowest-energy conformer for a Lig4 clamp interacting compound (compound #231) from the docking step. The clamp is represented in cartoon and residues making contacts with the molecule # 231 are highlighted and colored as in Fig. 1C. H-bonds are represented in black dashed lines.
