Scoring functions overview

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. 

Table 7.2 Overview of Currently Used Scoring Functions...

Table 7 Overview of frequently used scoring functions...

The SAR index (SARI) provides a composite score of individual SAR continuity and discontinuity functions, which have been introduced by Peltason et al. [83,47]. However, in order to identify activity cliffs, local scoring functions focusing directly on SAR discontinuity in a local environment around a chemical structure of interest are more informative than global activity landscape overviews. Regions of SAR discontinuity provide a lot of information on the SAR of a particular chemical series for deriving a pharmacophore hypothesis. For this case, the compound discontinuity score was introduced [80]. This variation of the SARI formalism is aiming to quantify individual molecular contributions to local SAR discontinuity. Typically, the... 

Fig. 1. Overview of motif discovery using network-level conservation. On the left, TGATAAG is given a high conservation score, because there are many pairs of orthologs that contain the k-mer in their upstream region. Consequently, TGATAAG is likely to be functional. On the other hand, AAAAAAA is given a low conservation score as the sets of upstream regions that contain it do not significantly overlap.

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