During the development of this algorithm we have made the following assumptions:
- we know the short amino acid sequence of one protein, which takes an active part in binding to another protein, with formation large numbers nearly located interacting amino acid residues, for example, the formation of homodimers Mdm2−Mdm2 and Nap1−Nap1,
- we do not know the active site of the whole protein responsible for binding to the short polypeptide sequence.
Thus, using algorithm 1, we find the active site on the polypeptide sequence of the whole protein. This algorithm presents two vectors: