![]() ![]() An approach for structural comparisons, fundamentally different from those using RMSD, was proposed by Rogen and Fain ( 10). They introduced the SGM (Scaled Gauss Metric), which is a metric derived from knot theoretical ideas to cluster proteins according to their structural topologies. ![]() They applied their method to predicting membership of proteins in CATH and achieved 95% accuracy at all levels of the classification hierarchy. In order to achieve a high level of agreement with other clustering schemes, some algorithms that use a multi-criterion approach (weighted combination of different scoring schemes), are initially trained on labeled data from an existing structural hierarchy (SCOP or CATH) and use cross-validation (or similar methods) to select the best parameters for their classifiers. ![]() ![]() For example, ProtClass ( 11) uses a nearest-neighbor-based classification scheme and several structural features to classify proteins at the fold level of the SCOP hierarchy. Their features include secondary structure elements predicted by the Stride program ( 12), the sequence length, and the percentage of observed helices. SCOPmap ( 13) is an approach that achieves roughly 95% accuracy when classifying proteins into the superfamily level of the SCOP hierarchy. ![]()
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