Originally, computational blind docking (BD) was introduced as a fast approach for finding binding positions and conformations of ligand molecules via scanning the entire surface of target molecules. BD can find not only primary binding sites but also allosteric or prerequisite ones. Since the introduction of BD in 2002, it has gained numerous applications in drug design. A combination of advanced molecular dynamics techniques with BD has yielded new, systematic methods for prediction of structures of target-ligand complexes at atomic resolution. Molecular dynamics also allows the use of explicit hydration models and helps distinguishing between binding modes of different target-ligand binding affinities. The present lecture features new results in method development and applications of BD in comparison with experimental structure determination methods.
Audience take away:
Computational docking is a key technique of target-based drug design at numerous pharmaceutical companies and research institutions. Besides routine docking applications in high throughput screening, blind docking can also detect allosteric binding sites which play an important role in e.g. anti-cancer drug discovery. This approach is also useful for understanding dynamics of target-ligand interactions and mapping of drug binding pathways at atomic resolution.