Discusses features, algorithms used, and scoring functions for pharmacophore generation. Also, it covers how databases are searched and created. Moreover, it includes a small discussion of field-based pharmacophores, and evaluation methods. Article discusses some of the main issues associated with pharmacophores including problems with molecular alignment, the need for new validation standards, difficulties when deciding which features to use, (e.g., which atoms should be considered hydrophobic), and that variable binding modes should be considered.
Leach, Andrew R., Valerie J. Gillet, Richard A. Lewis, and Robin Taylor. “Three-Dimensional Pharmacophore Methods in Drug Discovery.” Journal of Medicinal Chemistry 53, no. 2 (2010): 539–58.
Discusses features, algorithms used, and scoring functions for pharmacophore generation. Also, it covers how databases are searched and created. Moreover, it includes a small discussion of field-based pharmacophores, and evaluation methods. Article discusses some of the main issues associated with pharmacophores including problems with molecular alignment, the need for new validation standards, difficulties when deciding which features to use, (e.g., which atoms should be considered hydrophobic), and that variable binding modes should be considered.