Fig. 1

Similarity types and similarity-based features. A Ligand similarities include chemical similarities based on linear fingerprints, chemical similarities based on MOLPRINT2D fingerprints, and collaborative similarities. Receptor similarities include collaborative similarities, similarities calculated from sequence identity matrices, and from sequence similarities derived from BLOSUM62 substitution matrix. Sequence similarities were calculated based on the full protein sequence and based on the binding site sequences. Colored circle: red—the ligand does not activate the receptor, green—the ligand activates the receptor. Unknown associations are represented as blank spaces in the matrix. B Collaborative similarities for pairs of ligands and pairs of receptors, calculated based on known associations using Jaccard similarity. C Four similarity features are computed for ligands: the highest similarity to the ligand that activates \(r\), sum of similarity values to all ligands that activate \(r\), the highest similarity to the ligand that does not activate \(r,\) and the sum of similarity values to all ligands that do not activate \(r\). D Similarity based features are computed for the receptor: the highest similarity to the receptor that is activated by \(l,\) the sum of similarities to receptors that are activated by \(l\), the highest similarity to the receptor that is not activated by \(l,\) and the sum of similarities to receptors that are not activated by \(l\)