tbxzq-LigandScoringProtocol.txt

Name

CDVS score

Software

Glide 6.1

Parameters

None

Method

Poses for 102 FXR ligands were predicted using our cross-docking based virtual screening protocol. Single pose was predicted based on our cross-docking based pose prediction method. Glide 'Docking Score' score was then used to prepare rankings.

tbxzq-PosePredictionProtocol.txt

Name

CDVS

Software

Omega 2.5.1
ROCS 3.2.1
LigPrep 2.8
Glide 6.1

System Preparation Parameters

None

System Preparation Method

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.

Pose Prediction Parameters

None

Pose Prediction Method

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. In addition, all the FXR co-crystal structures released after the completion of D3R GC2 phase 1 were also included. 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 in hierarchical manner. Ligands were prepared using LigPrep. Only single final pose was predicted.