Molecular Dynamics Simulation of GPR34 inverse agonist comp. 15 and antagonist comp. 1

The initial protein structure was prepared using the Protein Preparation Wizard, and the ligands were generated with LigPrep. Both complexes were embedded in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer, solvated with TIP3P water molecules, and neutralized with 0.15 M NaCl. The MD was performed in the NPγT ensemble at 300 K using Langevin dynamics.

Long-range electrostatic interactions were computed using the u-series algorithm.10 runs of 100 ns MD simulation are contained for each ligand-receptor complex. The format of trajectories and topology files are transformed using VMD2.0b1 [1].The contacts are given by the program GetContacts (getcontacts.github.io/). The ligand-protein contacts, and the residue-residue contact adjacent to ligand binding site were extracted and visualize by flareplot (gpcrviz.github.io/flareplot).[1] Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual  Molecular Dynamics', J. Molec.