Figure 11

An example of Interface Residue Prediction using NPS-HomPPI. The sequence of the query protein 1 byf chain A is BLASTed against nr_pdb_s2c database. In this case, 3 sequences meet the thresholds set by NPS-HomPPI for "close homolog" in Safe Zone or Twilight Zone defined in Table 1. If there are more than K = 10 homologs met the zone thresholds in Table 1, regression equation 1 is used to determine the nearest K homologs for final prediction. For each position in the alignment, an amino acid residue in the query sequence is predicted to be an interface residue if the majority of the amino acid residues in the alignment are interface residues. Otherwise, it is predicted to be a non-interface residue. Interface residues are denoted by red 1's; Non-interface residues are denoted by black 0's. Question marks denote residues for which coordinates are missing from PDB files.