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Homology modeling has been applied to fill in the gap in experimental G protein-coupledreceptors(GPCRs)structure determination.However,achievement of GPCR homologymodels with ligand selectivity remains challenging due to structural diversity of GPCRs.Inthe present work,we propose a novel strategy by integrating pharmacophore and membranemolecular dynamics(MD)simulations to improve homology modeling of GPCRs with ligandselectivity.