Nowadays, computer-aided drug discovery (CADD) concepts are routinely used in academia and industry for identifying and optimizing lead structures. While CADD techniques have been widely used to attain a qualitative understanding of ligand binding to proteins, a current challenge is to quantify their interaction in a reasonable amount of time. One major issue is that the protein in reality can adapt its shape and properties upon each individual ligand binding to it (induced protein fit). In this context, I will present our development of new concepts incorporating protein flexibility to identify binding modes for ligands of biomedical interest and to quantify their interaction with the target protein. Based on examples from lead optimization and the prediction of adverse drug reactions, I will discuss our progress and current limitations.
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