Classification of all proteins with solved 3D structure using predicted helix architectures in comparison to the HISSdb database.

Helix interactions were predicted using the threshold combination C = 9 (network NN4) and C = 15 (network NN4-D), see Materials and Methods. HISS scores were calculated with and without edge weighting. Final classifications were obtained by clustering all proteins satisfying the specified HISS score thresholds using the MCL algorithm.aHISS scores were calculated both without weighting helix interactions (uw) and with up weighting interactions involving >15 residue contacts by a factor 1.5 (w).bAvg(HISS)same: average HISS score for proteins classified to the same helix architecture type in HISSdb.cAvg(HISS)diff: average HISS score for proteins classified to different helix architecture types in HISSdb.dAUC: area under the curve describing how well proteins with the same fold can be differentiated from proteins with different folds (AUC = 0.5 would correspond to a random prediction).eScore: HISS score threshold used for clustering proteins with the MCL algorithm. For both weighted and unweighted HISS scores, two thresholds were selected such that the specificity of the obtained classifications most closely approached either 80% or 90%.fSensitivity: Fraction of all protein pairs with the same HISSdb architecture annotation assigned to the same MCL cluster.gSpecificity: Fraction of all protein pairs with different HISSdb architecture annotation assigned to different MCL clusters.