Scoring functions

Bdhm H-J 1994 The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure J. Comp.-Aided Mol. Design 8 243-56... 

Method Ligand jfexibiUty sampling Scoring function... 

The calculation of the binding affinity with con.sidcration of all tbc.se effects for virtual screening is not possible. In order to circumvent thus difficulty, scoring functions arc used instead, c.g., the Liidi scoring function [80, or consensus scoring functions derived from FlevX score, DOCK score, GOLD score, ChemScore, or PMF score [81 ]. 

Rognan published the scoring function FRESNO (fast free energy scoring function), which considers a hydrogen-bond term, a lipophilic terra, a repulsive term for the buried polar surface, a rotational term, and a desolvation terra [82]. 

Fig. 12.23 Two simple scoring functions used in docking. On the left is the basic scoring scheme used by the DOCK program [Desjarlais et al. 1988], On the right is the piecewise linear potential [Cclhaar et al. 1995],...

Eldridge M D, C W Murray, T R Auton, G V Paoliniand R P Mee 1997. Empirical Scoring Functions 1 The Development of a Fast Empirical Scoring Fimction to Estimate the Binding Affinity of Ligand in Receptor Complexes. Journal of Computer-Aided Molecular Design 11 425-445. 

An additional role of the model evaluation methods is to help in the actual modeling procedure. In principle, an improvement in the accuracy of a model is possible by incorporating the quality criteria into a scoring function being optimized to derive the model in the first place. 

RH Lathrop, TE Smith. Global optimum protein threading with gapped alignment and empirical pair score functions. I Mol Biol 255 641-665, 1996. 

Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking an overview of search algorithms and a guide to scoring functions. Proteins 2002 47 409-43. 

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

Raha K, Merz KM. Large-scale validation of a quantum mechanics based scoring function predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J Med Chem 2005 48 4558-75. 

Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997 268 209-25. 

Liang SD, Grishin NV. Effective scoring function for protein sequence design. Proteins 2004 54 271-81. 

As discussed in the introduction, scoring functions still pose problems (see also Chapter 14). Some of these problems arise from insufficient consideration of details of favorable and unfavorable protein-ligand interactions. 

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