Scoring functions comparison

The current weaknesses of existing scoring functions are best illustrated by the observation that all available docking programs are using somewhat different scoring functions. Comparison studies of scoring functions have appeared in the recent... 

Pearlman, D. A. Charifson, P. S., Are free energy calculations useful in practice A comparison with rapid scoring functions for the p38 MAP kinase protein system, J. Med. Chem. 2001, 44, 3417-3423... 

Clearly, the quantitative methods for describing binding site similarities, required for large-scale database searches in the spirit of omics efforts, still need to be improved. The development of powerful scoring functions is an area of ongoing research, and hopefully some of the shortcomings will be resolved in the near future. Nevertheless, the examples discussed in this section demonstrate, within the realms of possibility, the usefulness of binding site comparison methods. 

Seeding experiments allow for comparisons of different scoring functions with respect to their performance for different targets. Seeding experiments... 

Table 10.2 Comparison of predictive power of EnTess models with that obtained with alternative scoring functions.

Kann, M. and R. A. Goldstein, Optimizing for success A new score function for distantly related protein sequence comparison, in RECOMB2000. 2000. Tokyo ACM Press. 

Fdgar, R.C. and Sjolander, K. (2004) A comparison of scoring functions for protein sequence profile alignment Bioinformatics (Oxford, England), 20 (8), 1301-1308. 

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