Explains the methods used by the Ligand Scout software. First, PDB files need to be treated to determine hybridization states, functional groups, and double bonds. Next, features such as hydrogen bond interactions are chosen based on a certain tolerance like the distance and angles. All features are represented by a sphere of 1.5 Å radius. Finally, different pharmacophore models are generated and then aligned to form one that can be used for virtual screening.
Paper also explains how pharmacophores were generated for Human Rhinovirus Serotype 16 Inhibitors and Tyrosine Kinase Inhibitors.
Wolber, Gerhard, and Thierry Langer. “LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters.” Journal of Chemical Information and Modeling 45, no. 1 (2005): 160–69.
Explains the methods used by the Ligand Scout software. First, PDB files need to be treated to determine hybridization states, functional groups, and double bonds. Next, features such as hydrogen bond interactions are chosen based on a certain tolerance like the distance and angles. All features are represented by a sphere of 1.5 Å radius. Finally, different pharmacophore models are generated and then aligned to form one that can be used for virtual screening.
Paper also explains how pharmacophores were generated for Human Rhinovirus Serotype 16 Inhibitors and Tyrosine Kinase Inhibitors.