Easy Does It: Reducing Complexity in Ligand-Protein Docking

Computational methods in structure-based drug design are used in a number of applications, including prediction of the structure of ligand-protein complexes also known as the docking problem, estimation of ligand-protein binding affinity, and in de novo design. Depending on the level of detail incorporated into the model, as well as the number of times the calculation is performed, the computational demands of these studies range from a few seconds on a small workstation to months on dedicated supercomputers. In the pharmaceutical industry, the criterion for a useful computational technique is simple: it must provide information of sufficient quality to impact the discovery or optimization of lead compounds, and it must do so in a timely manner.