Modeling water molecules in protein-ligand docking using GOLD.

By Marcel L. Verdonk, G. Chessari, Jason C. Cole, M. Hartshorn, Christopher W. Murray, J. Willem, M. Nissink, Richard D Taylor, Robin Taylor. Journal of Medicinal Chemistry, 2005

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Virtual ligand screening: strategies, perspectives and limitations (2006, background): “In the docking tool GOLD, water molecules can be switched on or off, and can spin around their principal axes to achieve good contacts with a docked ligand [106].”
Protein–ligand docking: Current status and future challenges (2006, background): “Verdonk et al.78 have implemented a novel approach to score water mediation and displacement in the docking program GOLD.”
Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites (2012, positive): “Some docking procedures, although different in implementation, involve switching explicit water molecules ‘‘on’’ and ‘‘off’’ [17,60,61].”
rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids (2014, methodology): “The current version has prototype code to sample fully the degrees of freedom and occupancy of interstitial water molecules, as previously described for GOLD [29], or to dock simultaneously to an ensemble of receptor coordinates to simulate receptor flexibility in an efficient way.”
Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock (2009, methodology): “In recent years, progress has been made in developing docking algorithms that predict ligand binding to proteins and by now several docking programs are available such as AutoDock, [3,4], GOLD, [5,6], Glide, [7,8] and FlexX [9,10].”