2026-10-12T23:01:28Z https://www.scidb.cn/oai

10.57760/sciencedb.012ds 2026-09-15T11:22:01Z

2026-09-15 Molecular Dynamics Simulation of GPR34 inverse agonist comp. 15 and antagonist comp. 1 doi:10.57760/sciencedb.012ds en This dataset contains the molecular dynamics (MD) simulation data of the G protein-coupled receptor GPR34 in complex with an inverse agonist (comp. 15) and an antagonist (comp. 1).The systems were constructed, simulated, and analyzed using Maestro 2025-4 (Schrödinger Release 2025-4). 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 (https://getcontacts.github.io/). The ligand-protein contacts, and the residue-residue contact adjacent to ligand binding site were extracted and visualize by flareplot (https://gpcrviz.github.io/flareplot).[1] Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual  Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38. Molecular Dynamics; GPR34; G-protein coupled receptor; Inverse Agonist; Antagonist Tomohiko Ohwada Chen Luying Huang Junjun EMBARGO https://creativecommons.org/licenses/by/4.0/ dataset Science Data Bank