Binding sites between Fe-protein and MoFe-protein.

<p>Binding sites inferred on α (a) and β (b) subunits of MoFe protein, PDB chain 1MIO_A and 1MIO_B respectively. Two helical regions assumed to be critical for interaction are shown in magenta. Binding site residues are shown by side chains (in red color) and match with residues predicted by Kim at al. Binding site residues shown in yellow on α subunit (1MIO_A) are part of inserted 50 residues sequence and are not predicted by IBIS.</p

Comparison of IBIS with other protein-protein interaction prediction methods.

<p>Here N_p and N_c represent the number of total and correctly predicted binding site residues respectively. N_t is the number of true binding site residues. HomPPI was queried using the test set of 188 chains. Note that IBIS was able to make predictions for only 146 chains, as for the remaining 25 cases there were no homologous structural complexes above the 30% identity cutoff. For these 25 cases we considered the number of correctly predicted binding site residues to be zero penalizing the estimated IBIS accuracy even though by definition IBIS could not provide predictions for these cases.</p

Overview of IBIS.

<p>Overview of IBIS.</p

Percentage and frequency of CDD annotated binding sites predicted by IBIS at a given rank.

<p>Percentage and frequency of CDD annotated binding sites predicted by IBIS at a given rank.</p

Specificity and sensitivity of IBIS to predict protein-protein interaction.

1<p>Specificity drops to 67% when interactions from singleton clusters are also considered.</p>2<p>Sensitivity drops to 68% when interactions from only conserved clusters are considered.</p

Reconstructing biounits by homology inference.

<p>Recovery of those homooligomeric interfaces by IBIS which can only be produced by applying crystallographic symmetry operations to PDB ASU. Recovery rate is calculated as a number of binding site residues identified by both PISA and IBIS divided by the number of binding site residues identified by PISA by applying crystallographic symmetry operations.</p