The expected IC20 was computed by calculating the synergy between two drug compounds based on their individual activity.
In the framework of the DSI method, a measure to represent the distance between two compounds is determined based on the protein-compound affinity matrix.
We computed the chemical structure similarities between compounds using SIMCOMP (Hattori et al., 2003), a program that finds the common substructures between two compounds and outputs the global similarity score based on a graph alignment algorithm.
The main reason is that the confidence score of an interaction between two compounds, which was used in the method based on chemical interactions, contains different kinds of information of compounds, such as their activities, structures, reactions, and so forth [ 18], while the method based on chemical similarities only used the information of compound structures.
We computed the chemical structure similarities between compounds using SIMCOMP (Hattori et al., 2003), where SIMCOMP provides a global similarity score based on the size of the common substructures between two compounds using a graph alignment algorithm.
The CI between two compounds A and B is: CI = C A, X I C X. A + C B, X I C X. B Based on CI values, the extent of synergism/antagonism was determined.
Calculation of the shortest path between two compounds using the reaction graph considers the two links that join two compounds to a reaction as a single link.
In this study, we screened three essential oils and four pure compounds based on eugenol for acaricidal properties.
The top three TCM compounds based on the ranking of docking by Discovery Studio 2.5 were selected as candidate compounds for molecular dynamics investigation.
Our results highlight subtle differences between these two classes of compounds based on the MS fingerprints, enabling confidence differentiation of the compounds.
