Molecular modeling of interaction between antihistamines and retinoid acid receptor beta

This dataset contains a series of PDB files that depict the most likely interactions between antihistamines and retinoid acid receptor beta, predicted by Desmond molecular dynamics simulation.Preparation of retinoic acid receptors for molecular dockingBond orders and hydrogenation for the complex structures were assigned using Protein Preparation inMaestro. The ionization states within pH 7.0 ± 2.0 were generated using Epik in Maestro. Hydrogenbond optimization was performed using PROPKA in Maestro. Energy minimization was done withOPLS3e force field setting. Loop structures were refined using Loop Refinement feature in Maestro.High-throughput virtual screening was performed using Glide in Maestro.MD simulationMD simulations for interaction analysis and binding free energy calculation were performed usingDesmond (Schrödinger Inc., USA). All systems were set up using “System Builder” software in Maestro.The RARβ-9-cis-RA (agonist control) and RARβ-antihistamine complexes were placed in the orthorhombic box with a buffer distance of 10 Å to create a hydration model using the SCP water model. The following parameters wereset: cut-of radius for van der Waals interaction, time step, initial temperature, and pressure of thesystem set to 9 Å, 2.0 fs, 300 K, and 1.01325 bar, respectively. The sampling interval during thesimulation was set to 100 ps. Finally, we performed MD simulations under the NPT ensemble for 100nanoseconds.