A formal approach to molecular docking

• Authors: Davide Prandi
• Venue: CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
• Year: 2006

Drugs are small molecules designed to regulate the activity of specific biological receptors. Design new drugs is long and expensive, because modifying the behavior of a receptor may have unpredicted side effects. Two paradigms aim to speed up the drug discovery process: molecular docking estimates if two molecules can bind, to predict unwanted interactions; systems biology studies the effects of pharmacological intervention from a system perspective, to identify pathways related to the disease. In this paper we start from process calculi theory to integrate information from molecular docking into systems biology paradigm. In particular, we introduce Beta-binders${^\mathbb D}$, a process calculus for representing molecular complexation driven by the shape of the ligands involved and the subsequent molecular changes.