Fig. 1.

The IsItABarrel algorithm. (A and B) Structures are colored from N to C terminus using rainbows from blue to red. Probability of contact is indicated by pixel gray value, with darker pixel indicating stronger contact between residues in x and y axis. (A) OmpT (PDB ID: 1I78) (Left) and corresponding contact map predicted by RaptorX-Contact (Right). The map shows typical features of β-barrel proteins, antiparallel contacts between neighboring strands (green circle) and the closing contact between the first and last strands of the barrel (purple circle). (B) Structure of the non-TMBB armadillo-repeat protein (PDB ID: 4V3O) (Left) and corresponding contact map predicted by RaptorX-Contact (Right) without the typical features found in maps of β-barrels. (C) Strand–strand interaction (β-hairpin) detection. Map is scanned along the main diagonal in search of β-hairpins. Detected β-hairpins are characterized in terms of the length of their contact network (Inset). The sum of the contact probabilities along a successfully detected β-hairpin is compared against the threshold for inclusion in the final TMBB classification step. (D) A closing contacts line is detected that aligns with the first and last strands. (E) Classification by IsItABarrel is a two-step process requiring either a closing contact or four hairpins. (F) Sequences sharing more than 40% identity tend to have the same IsItABarrel classification. Percentage of pairs that share the same IsItABarrel prediction (y axis) for each bin of percent similarity (x axis) (purple), total number of comparisons (log₁₀) at each similarity level (gray). Dashed line at 40% pairwise sequence similarity. (G) Steps the algorithm used to assign IsItABarrel predictions by similarity. A large set of sequences is clustered by sequence similarity. IsItABarrel predictions are made for the cluster representatives. Cluster members are assigned the same prediction as their cluster representative.