Motivation: Networks to predict protein pharmacology can be created using ligand similarity or using known bioassay response profiles of ligands. Recent publications indicate that similarity methods can be highly accurate, but it has been unclear how similarity methods compare to methods that use bioassay response data directly. Results: We created protein networks based on ligand similarity (Similarity Ensemble Approach or SEA) and ligand bioassay response-data (BARD) using 155 Pfizer internal

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... BioPrint assays. Both SEA and BARD successfully cluster together proteins with known relationships, and predict some non-obvious relationships. Although the approaches assess target relations from different perspectives, their networks overlap considerably (40% overlap of the top 2% of correlated edges). They can thus be considered as comparable methods, with a distinct advantage of the similarity methods that they only require simple computations (similarity of compound) as opposed to extensive experimental data.