autodock-vina

docking of small molecules to proteins
  https://vina.scripps.edu
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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.

The same institute also developed autodock, which is widely used.

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