In order to understand the mechanisms of ligand binding and the interaction between the ligand and the Human Neurokinin receptors NKR1, NKR2 and NKR3, three-dimensional (3D) models of the three receptors are generated based on the crystal structure of the bovine rhodopsin (PDB code 1u19A) by using Modeller. Accordingly 25 models are generated and the model having lowest modeler objective function was choosed for the further assessment. The models thus generated are assessed using ProSa II and Procheck. The results show that the models are reliable. With the generated models, a flexible docking study was performed. The docking results indicated the conserved residues involved in antagonist binding. The interactions proposed in this study are useful to understand the potential mechanisms of the respective antagonists used in the study.
Homology Modeling, Docking, Neurokinin Receptors, Modeller, AutoDock, ProSa, Procheck
