1st scenario

presents the common SAR task when the program predicts protein targets for the query ligand by comparing with chemical structures of compounds with known target spectra.

Ligand-based prediction

2nd scenario

searches the small molecule ligands for the test protein by comparing the amino acid sequences with known ligands. Ligands’ structures are not considered.

Sequence-based prediction

3rd scenario

is applied in the absence of the information on interaction spectra of both the target and ligand. The predictive algorithm requires the protein sequence and ligand structure.