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Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data

Figure 1

Residue pair and single-residue contact data preparation from ligand/receptor complexes (an example with a dimeric ligand complexed with a dimeric receptor is shown here).

For each of the 124 complexes, the data sets were prepared by pairing residues from the ligand and receptor chains for a pair-wise prediction (as shown in the second part of the illustration). Single-residue data were also prepared for the whole complex. However, the residues were not encoded as pairs; they were taken from individual chains and partner information was discarded, and the contact data for all the chains were pooled together to obtain whole-complex data. In one training cycle, the contact and feature data from all but one of the complexes were used for training, and the left-out complex data were then used to evaluate prediction performance. Performance scores were calculated for one complex in one training cycle. The obtained set of 124 scores was then averaged to obtain an overall performance score.

Figure 1