docking of small molecules to proteins

 AutoDock Vina is a program to support drug discovery, molecular
 docking and virtual screening of compound libraries. It offers
 multi-core capability, high performance and enhanced accuracy
 and ease of use.
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 The same institute also developed autodock, which is widely used.
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 O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy
 of docking with a new scoring function, efficient optimization and
 multithreading, Journal of Computational Chemistry 31 (2010) 455-461