Abstract
A pharmacophore represents a simple and intuitive concept that can be used in many different drug discovery applications. Ligand-based and structure-based pharmacophore models continue to play a pivotal role in hit discovery and may guide lead optimization. Moreover, owing to the versatility of the pharmacophore concept, pharmacophore modelling has been routinely used in combination with other molecular modelling techniques. The synergistic use of different tools in drug discovery workflows may allow to fully exploit the advantages, while compensating for some of the intrinsic limitations, of each methodology. This review will focus on the synergistic combination of pharmacophore modelling with other molecular modelling approaches such as the hot spot analysis of protein binding sites, molecular dynamics, and docking.
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