LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters
- PMID: 15667141
- DOI: 10.1021/ci049885e
LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters
Abstract
From the historically grown archive of protein-ligand complexes in the Protein Data Bank small organic ligands are extracted and interpreted in terms of their chemical characteristics and features. Subsequently, pharmacophores representing ligand-receptor interaction are derived from each of these small molecules and its surrounding amino acids. Based on a defined set of only six types of chemical features and volume constraints, three-dimensional pharmacophore models are constructed, which are sufficiently selective to identify the described binding mode and are thus a useful tool for in-silico screening of large compound databases. The algorithms for ligand extraction and interpretation as well as the pharmacophore creation technique from the automatically interpreted data are presented and applied to a rhinovirus capsid complex as application example.
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