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Combenefit / Combinations Benefit
Offers advanced graphical capabilities and allows for model-based quantification of drug combinations in single and high-throughput settings. Combenefit enables the visualisation, analysis and quantification of drug combination effects in terms of synergy and/or antagonism. Data from combinations assays can be processed using classical Synergy models (Loewe, Bliss, HSA), as single experiments or in batch for high throughput screens. This user-friendly tool provides laboratory scientists with an easy and systematic way to analyse their data. The companion package provides bioinformaticians with critical implementations of routines enabling the processing of combination data.
SynergyFinder
Serves for pre-processing and visualization of the drug combination dose-response data. The tool implements synergy scoring with four major reference models: (i) HSA model, where the synergy score quantifies the excess over the highest single drug response; (ii) Loewe model, where the synergy score quantifies the excess over the expected response if the two drugs are the same compound; (iii) Bliss model, where the expected response is a multiplicative effect as if the two drugs act independently; and (iv) ZIP model, where the expected response corresponds to an additive effect as if the two drugs do not affect the potency of each other.
Synergy Maps
Allows integration of information about the synergistic interactions of compounds with information about their properties (chemical structure, physicochemical properties, bio-activity profiles) to produce a single visualization. As a result the relationships between compound and combination properties may be investigated simultaneously, and thus may afford insight into the synergy observed in the screen. An interactive web app implementation called Synergy Maps, developed for public use, allows straightforward exploration of combination data, and easier identification of correlations between compound properties and interactions.
PDOD / Prediction of Drugs having Opposite effects on Disease genes
Identifies drugs having opposite effects on altered states of disease genes. PDOD proposes a scoring function to discover drugs likely to restore altered states of disease genes using the path from a drug to a disease through the drug-drug target interactions, shortest paths from drug targets to disease genes in molecular pathways, and disease gene-disease associations. The method provides a simple web service that researchers can submit genes of interest with their altered states and will obtain drugs seeming to have opposite effects on altered states of input genes.
Genedata Screener
A software tool designed for fast and efficient analysis of compound combination experiments. Dedicated calculation methods together with visualization methods such as heat maps and isobolograms enable assessment of combination effects, and the inherent automation, standardization, and flexibility of Genedata Screener provide excellent performance and streamlined workflows. Interactive calculation and visualization configuration combined with robust fitting produce better results in shorter time.
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