Prediction of protein-ligand interactions. Docking and scoring: successes and gaps.

By Andrew R. Leach, Brian K. Shoichet, C. E. Peishoff. Journal of Medicinal Chemistry, 2006

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Docking & Chemoinformatic Screens for New Ligands and Targets (2009, background): “In the last decade, however, the use of structure-based computational design has made steady, if often unspectacular [2] technical progress, to the point where most pharmaceutical organizations have substantial groups devoted to its application.”
An interaction-motif-based scoring function for protein-ligand docking (2010, background): “Despite fundamental fallacies in this assumption, it has been adopted for many years, as otherwise the problem would be intractable or too computationally expensive to handle practically [21,22].”
High quality binding modes in docking ligands to proteins (2008, background): “18–22 Accounting for protein flexibility is a difficult task, due to the huge solution space, with many additional degrees of freedom compared with ligands.”
In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling (2007, background): “…in target sites is still a challenging process after more than 20 years of research in the field (Kitchen et al ., 2004; Ghosh et al ., 2006; Leach et al ., 2006) and the performance of different implementations has been found to vary widely depending on the given target (Cummings et al .,…”
Virtual Screening with AutoDock: Theory and Practice (2010, background): “Building on 2 decades of research, many successful methods for docking of ligands to macromolecular targets have been developed [6-13].”