In drug discovery, the receptor structure is often unknown, but the ligand structure is known. If only a single active molecule is known, it is impossible to map the key contributing pharmacophore characteristics to the molecule, and the only option may be to use similarity queries (eg, using pharmacophore fingerprints) to retrieve similar molecules. When active ligands with a set of different skeletons of known structure are available, ligand-based pharmacophore modeling can be used. The clarification of the pharmacophore involves two steps. First, the conformational space of flexible molecules needs to be widely covered because the biologically active conformation is unknown. Second, the molecules need to be compared by common pharmacophore characteristics, which can be retained in the 3D model. Ligand-based Pharmacophore Model https://www.computabio.com/ligand-based-pharmacophore-model-service.html
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