Table 1.
Tools used to analyze drug combination data.
| Tool name | Tool type | Reference model(s) | Input data | Brief description |
|---|---|---|---|---|
| CompuSyn [25] | Free software | Loewe additivity model | Dose-response data | CompuSyn only allows for manual input of one drug combination at a time |
| Synergyfinder [26] | R package | HSA, Loewe additivity, Bliss independence | Dose-response data | Synergyfinder is implementations for all the popular synergy scoring models for drug combinations, including HAS, Loewe, Bliss, and ZIP [10] |
| Mixlow [27] | R package | A nonlinear mixed-effects model | Dose-response data | Mixlow used a nonlinear mixed-effects model to estimate parameters of dose-response curves and required experimental design where the ratio of two drugs in a combination is fixed |
| COMBIA [28] | R package | Bliss independence, Loewe additivity | Data from wet-lab experimental | Data from wet-lab experimental platforms can be directly used |
| MacSynergyII [29] | Free software | Bliss independence | Dose-response data | MacSynergy II is essentially an Excel file and it scales the input data to %inhibition using positive and negative controls |
| Combenefit [30] | Free software | HSA, Loewe additivity, Bliss independence | Dose-response data | Combenefit has advanced graphical capabilities and can be applied to model-based quantification of drug combinations in single and high-throughput settings |
| Combinatorial Drug Assembler [31] (http://cda.i-pharm.org/) | Free web app implementation | None | Disease-related signaling pathway components | CDA performs expression pattern matching between input gene sets and 6,100 molecule-treated expression profiles of the connectivity map to list up best pattern matching single drugs/combinatorial drug pairs |
| Synergy Maps [32] (http://richlewis42.github.io/synergy-maps/) |
Free web app implementation | None | Drugs or drug combinations in two datasets [25, 26] | Synergy Maps can simultaneously represent individual compound properties and their interactions |
| DT-Web [33] (http://alpha.dmi.unict.it/dtweb/) |
Free web app implementation | None | The name or the accession number of a drug/target | A web-based application for drug-target interaction and drug combination prediction |
| TIMMA-R [34] | R package | Logic-based network | Drugs' polypharmacological profiles and drug sensitivity profiles from a given cancer cell line | TIMMA-R predicts the effects of drug combinations based on their binary drug target interactions and single-drug sensitivity profiles |