As the number of protein crystal structures has increased so too has the interest in using this detailed structural knowledge for library design, compound acquisition and data analysis. Structure-based design methods have been developed over many years. However, much of this activity was geared towards methods for the detailed analysis of small numbers of molecules. Several factors have contributed to the move towards higher-throughput structure-based methods. First, high-performance computer hardware (often based on the linux operating system) has provided unparalleled amounts of dedicated computing power at a low cost to researchers. Second a significant effort has been expended in the development of new algorithms, particularly for molecular docking. Finally, tools for the analysis of the output of such calculations enable scientists to navigate more effectively through the large quantities of data generated.
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