From Protein Structure to Function with Bioinformatics.pdf

196 E.C. Meng et al.used in matching. An alpha-carbon-only description is less specific than one thatincludes side chain atoms. Three-dimensional motifs with fewer residues are lessspecific. Stringent match settings (only allowing residues of identical types topair, a low RMSD cutoff) can restrict results to closely related proteins even ifmeaningful matches to more distantly related proteins could be obtained withlooser criteria.Most methods provide numerical scores to rank hits and indicate match quality.For example, RMSD values indicate the geometric fit between points in a 3D motifand the corresponding points in a structure. RMSD is an appropriate measure forranking matches to a given motif, but it is not useful for comparing among motifsof different sizes. Further, some motifs are more likely to be matched merelybecause they contain more common residues. To account for these issues and providea better ranking of hits, some methods calculate statistical significance orexpectation values (e.g., p-values or E-values). Some limitations must be kept inmind, however, as these values depend on any underlying assumptions of a statisticalmodel and on the data used to parameterize the model.Regardless of how a 3D motif was generated, it can be evaluated against asample of structures. When the sample includes validated positive and negativeexamples, the results can be expressed in terms of sensitivity, the ability to identifythe positive examples, and specificity, the ability to exclude the negative examples.When the sample includes just negative examples, the resulting RMSD distributioncan be used to estimate the statistical significance of matches to that motif.The usefulness of these derived quantities depends on an adequately large andrepresentative sample.A consensus approach may be helpful, where multiple hits to related motifs orsimilar results obtained with different programs or databases (Table 8.1) may convergeto a common prediction.Finally, common sense must be applied. For example, there may be a significantmatch to an active site motif but no pocket for binding the substrate. Further, statisticalsignificance is not the same thing as biological significance – a biologicallysignificant motif may not score as statistically significant compared to a motif thathas no biological importance. Thus, it is prudent to inspect matches visually and toevaluate them using biologically relevant criteria before using them to infer functionor any other characteristic of a protein.8.3 Specific MethodsThe studies of 3D motifs can be described according to how they treat the problemof choosing motifs. First are those studies that focus on evaluating methods forfinding matches to any user-defined motif, and leave the problem of choosing a relevantmotif to the users of the method or later studies. Second are those studies thattreat motif discovery or generation of motif libraries as essential to their method, ifnot the primary goal of their method.