Docking, Virtual Screening and MD in Drug Discovery
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The use of computational methods had a major impact on modern drug design and is now firmly established as a necessary element of any drug development. A recent study by Boston Consulting estimated that the use of in silico methods saves approximately $130M off the current development cost of $880M for a typical drug. The most successful and widely used of these methods are the in silico screening of virtual libraries for lead discovery and the docking and MD simulation for lead refinement. The key elements of these computer applications to drug discovery can be categorized into bioinformatics techniques that do not require significant resources. In the docking, virtual screening, and scoring segment the interactions between the target protein and small molecule drug candidates are evaluated using empirical scoring functions (e.g. AutoDock, Dock, Flexx, Gold, or Glide) to calculate the binding energy and mode. Because these simple calculation do not consider protein flexibility, the most promising candidates are refined by molecular simulations (e.g. in CHarMM or Amber), ranging from 0.5 to 10 ns simulation time. NWICG resources are requested to support these calculations.

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