Scoring functions assessment

Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL. Assessing scoring functions for protein-ligand interactions. J Med Chem 2004 47 3032-47. 

A critical assessment of docking programs and scoring functions. JMed ChemA9, 5912-5931. 

All patients were monosensitized with a persistence of symptoms despite action to eliminate mites and treatment with inhaled corticosteroids. Patients were included after an 8-week observation period which made it possible to determine the lowest effective dose of budesonide, with the performance of skin tests, lung function tests and a methacholine bronchial challenge test. The efficacy criteria were the medication and symptom scores, global assessment of the patient by the physician, skin tests and total IgE, lung function tests and the methacholine bronchial challenge test. 

Warren GL, Andrews CW, Capelli AM et al (2006) A critical assessment of docking programs and scoring functions. J Med Chem 49(20) 5912-5931... 

Warren CL, Andrews CW, Capelli A-M, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS. A critical assessment of docking programs and scoring functions. J. Med. Chem. 2006 49 5912-5931. 

In most empirical scoring functions, a hydrophobic character is attributed to several atom types, with equivalent weight for all hydrophobic contributions. In a more sophisticated approach, the propensity of particular atom types to be solvent-exposed or embedded in the interior of a protein can be assessed by so-called atomic solvation parameters. These have been derived, for example, from experimental octanol/water partition coefficients (303, 304) or from protein crystal structures (305, 306). Atomic solvation parameters are used in the VALIDATE scoring function (307) and have been tested in DOCK (308). 

An objective assessment of the available scoring functions is difficult because only very few functions have been tested on the same data sets or with the same docking tool. For... 

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