Molecular Bioinformatics In Drug Discovery

Being the only representative structure, rhodopsin is the basis of homology modeling for the 7TMRs in many studies, of which some have spawned attempts at virtual screening. For many years, the molecular modeling community based their analyses on the low resolution electron microscopy (EM) structures of bacteriorhodopsin. Others attempted to derive models from the less well resolved bovine rhodopsin EM sources, using distance constraints from experimental data, MSAs, ligand specificities and presumed binding sites, or iterative procedures based on satisfying H-bond potentials. With the availability of the bovine rhodopsin crystal structure, and because of the limited superposition with bacteriorhodopsin, the in silico community has moved wholesale to rhodopsin-based models of GPCRs for virtual screening and drug discovery.

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