Читать книгу Computation in BioInformatics - Группа авторов - Страница 21

This is a powerful method which can easily categorize a group of molecules/ligands on the basis of active and inactive compounds. They provide set of molecular characteristics that is essential for the macromolecular recognition of ligands triggering a biological reaction. Some of the essential features modeled in pharmacophore are aromatic, hydrophobic, hydrogen bond acceptor (HBA), hydrogen bond donor (HBD), and anion and cation residues. Two main types of Pharmacophore modeling are structure-based modeling and ligand-based modeling.

Structure-based Pharmacophore modeling depends on the 3D structure of the protein obtained from PDB. These structures in PDB are provided by X-ray crystallography technique and/or NMR spectroscopy techniques. In the absence of 3D structure of protein, ligand-based Pharmacophore modeling is performed. Some of the softwares which are used for pharmacophore modeling are HypoGen, HipHop, DISCO, and PHASE.

 PHASE: It is a user friendly pharmacophore modeling solution for LBDD and SBDD. It creates hypotheses from protein-ligand complexes and apo proteins with Schrödinger’s unique e-Pharmacophores technology. It can be accessed at https://www.schrodinger.com › phase.