Docking and scoring

There have been several major papers published in this area, in which the difficult issues of the accuracy of docking and scoring methods are addressed. In an ideal case, we would want a docking program that could always generate the same pose of a ligand as observed in an X-ray complex, and a scoring function that would clearly rank this pose as the best. 

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Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery methods and applications. Nat Rev Drug Discov 2004 3(ll) 935-49. 

Eriesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Erancis P, Shenkin PS. Glide a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004 47 1739-49. 

Muegge I, Enyedy I. Docking and scoring. In Tollenaere J, de Winter H, Langenaeker W, Bultinck P, editors. Computational medicinal chemistry and drug discovery. New York Marcel Dekker. 2004. p. 405-36. 

Krovat EM, Steindl T, Danger T. Recent advances in docking and scoring. Curr Comput Aided Drug Des 2005 1 93-102. 

Ingo Muegge and Matthias Rarey, Small Molecule Docking and Scoring. 

Glide a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47(7) 1739-1749. 

Muegge, I. and Rarey, M. Small molecule docking and scoring. In... 

Muegge, I. and Enyedy, I. Docking and scoring. In Computational Medicinal Chemistry and Drug Discovery,... 

There has been considerable discussion on the validity of docking and scoring functions in structure-based design because of the complex issues involved such as ligand orientation, water participation, or flexibility of the target protein itself [186-190]. 

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