Project PI: Jagdish Patel
This research project is to identify the correct bound conformations of veranamine in signma-1 and 5HT2B receptors. Crystal coordinates of sigma-1 and 5HT2B receptors will be downloaded from the Protein Data Bank. Both of the receptor structures will then be used to perform ordinary molecular dynamics to sample various conformations available. Docking software will be used to dock veranamine to 100 snapshots obtained from molecular dynamics simulations of each receptor to determine the pocket heavily populated with high scoring poses. Highly populated pose of veranamine in both receptors will be refined using flexible docking to obtain the final best bound conformations. Structural analogs will be docked directly to the predicted binding site of veranamine using a docking software.