Explains in detail how pharmacophore features such as hydrogen bond donors/acceptors, hydrophobic areas, and positive and negative ionizable areas are defined by Ligand Scout. Moreover, it describes a classification of features based on specificity.
Additionally, a preprocessing method for PDB structures is shown. It consists in determining hybridization states, double bonds, rings, etc.
Wolber, Gerhard, and Robert Kosara. “Pharmacophores and Pharmacophore Searches.” Methods and Principles in Medicinal Chemistry, 2016, 131–50.
Explains in detail how pharmacophore features such as hydrogen bond donors/acceptors, hydrophobic areas, and positive and negative ionizable areas are defined by Ligand Scout. Moreover, it describes a classification of features based on specificity.
Additionally, a preprocessing method for PDB structures is shown. It consists in determining hybridization states, double bonds, rings, etc.