Scoring scheme

Fig. 10.16 Finding the optimal sequence alignment using dynamic programming with a scoring scheme in which a match scores 1, a mismatch scores —1 and the gap penalty is —2.

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],...

Sadowski J and H Kubinyi 1998. A Scoring Scheme for Discriminating Between Drugs and Nondrug Journal of Medicinal Chemistry 41 3325-3329. 

To demonstrate the excellent correlation (r- = 0.99) between the luminance of the images and molecular diversity, we plotted the luminance values of the map versus the mean similarity values of data sets (Fig. 4-13). From this plot, a scoring scheme for the classification of CSPs from specific to broad application range can be well established Crownpak CR > Pirkle DNBPG > Whelk > Chiralpak AD > Chiralcel OD. 

Sadowski J, Kubinyi H. A scoring scheme for discriminating between drugs and non-drugs. J Med Chem 1998 41 3325-9 (1998). 

The authors also evaluated the performance of various DES-T and DES cutoffs for detecting taxon members defined by Bayesian probabilities. Waller and Ross found that DES-T cutoffs work much better than the cutoffs on the DES because they have higher sensitivity, specificity, and positive and negative predictive values. One could say that the authors stacked the deck in favor of the DES-T, as the Bayesian probabilities and DES-T scores are based on the same data. However, this redundancy is unavoidable, since there is no other method of assessing taxon membership. It is important to evaluate the qualities of DES-T cutoffs for studies that will use the DES-T, rather than the Bayesian scoring scheme. 

These norms, of course, are not ideal. First, the Winnipeg sample may not be representative of the general population of the United States. Second, the sample size is too small to provide adequate general population norms. The reliability of estimates that the scoring scheme is derived from (e.g., taxon base rate, indicator validities) depends on the number of taxon mem-... 

D. Fenyo and R. C. Beavis. A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications using General Scoring Schemes. Anal. Chem., 75, no. 4 (2003) 16%-114. 

Table 15. Klimisch scoring scheme for reliability studies... 

The reader should note that this scoring scheme is the same one used for dermal sensitization scoring, whereas the scoring method for the rabbit model discussed previously is that used for dermal irritation studies.)... 

The third requirement is a scoring scheme to identify optimal dynamic programming alignments used in the above iterative multiple alignment... 

Represent the probability of observing the 20 amino acids in a randomly aligned position where all the types of amino acid residues were observed at least once. These probabilities are used with the log-likelihood scoring scheme. 

Karlin, S., and Altschul, S. F. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. U.S.A. 87, 2264-2268. 

Sadowski, )., Kubinyi, H.A. Scoring scheme for discriminating between drugs and nondrugs. J. Med. Chem. 1998, 43, 3325-3329. 

Pharmacophore similarity scoring schemes are represented by the FBPA and ComPharm overlay dissimilarity scores, the expectation being to see low dissimilarity scores matching high activity levels. 

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