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Table 1 A classification of systematic drug synergy prediction models

From: Systematic synergy modeling: understanding drug synergy from a systems biology perspective

Model type Description Inputs Methods Outputs
PPI network-based models Evaluate drug synergy based on network topology relations of targets Drug targets; Complex network; Synergistic drug combinations;
Protein interactions Network pharmacology Synergistic targets
Pathway-based models Simulate the dynamic changes of pathway and identify synergy-specific pathway structures Drug targets; Ordinary differential equations; Dose–response assessment of drug synergy;
Pathway structures; Network motif recognition Synergy-specific
Dynamic changes of each pathway component; network motifs in pathways
Drug interactions
Drug similarity-based models Construct classification models based on various drug similarities Drug properties like targets, structures, indication, et al. Similarity calculation; Synergistic drug combinations;
Feature selection; Distinctive features for drug combination
Classification model
Omic-based models Apply “omic” data to calculate drug associations; or rebuild the synergy-dependent pathways Responses to drugs in the form of “omic” data Reverse engineering of biological networks; Synergistic drug combinations;
“Omic” data similarity calculation; Biological networks;
Classification model