According to the authors structured-based pharmacophores are superior to ligand-base ones. This is because ligand models ignore intricate details of the binding site shape as well as interactions sites. Furthermore, structured-based pharmacophores followed by docking can provide superior results for finding new leads.
The article also offers a review of some of the most popular structured-based pharmacophore software. It states that the main weaknesses of these programs are that they cannot be applied in situations where only the target structure is available and that they lack the option to export pharmacophores to other programs.
Gaurav, Anand, and Vertika Gautam. “Structure-Based Three-Dimensional Pharmacophores as an Alternative to Traditional Methodologies.” Journal of Receptor, Ligand and Channel Research Volume 7 (2014): 27–38.
According to the authors structured-based pharmacophores are superior to ligand-base ones. This is because ligand models ignore intricate details of the binding site shape as well as interactions sites. Furthermore, structured-based pharmacophores followed by docking can provide superior results for finding new leads.
The article also offers a review of some of the most popular structured-based pharmacophore software. It states that the main weaknesses of these programs are that they cannot be applied in situations where only the target structure is available and that they lack the option to export pharmacophores to other programs.