Ligand conformations for shape similarity calculations were generated using Omega. A maximum number of 200 conformations per ligand was generated. Receptors for molecular docking were prepared using protein preparation utility of Maestro. Standard protein preparation procedure was followed.
Our method utilizes ligand 3D shape similarity with known co-crystal structure ligand to identify suitable receptors for molecular docking of ligands. For each ligand, our method identifies its suitable receptor and utilizes it for molecular docking calculations. All available ligand bound crystal structures of FXR protein from PDB were downloaded and were superimposed with target protein. Relevant ligands were extracted and ligand 3d shape similarity calculations between ligand conformations and crystal structure ligand were performed using ROCS program. Ligand conformations were generated using Omega program. Suitable receptors were selected based on high 3D shape similarity. These receptors were then used for molecular docking using Glide program. Both SP and XP version of program were used. Ligands were prepared using LigPrep.