Annotation of the Life Chemical stock compound library using several cheminformatic and full text mining approaches
This repository contains code and documentation to subset the Life Chemicals Stock compounds into custom collections. You can get a login to download the original files. The RDA files provided here are compressed .rda files from the R session containing the R data object of the sdfsets.
| Description | SDF | RDA |
|---|---|---|
| Stock1 | SDF | RDA |
| Stock2 | SDF | RDA |
| Stock3 | SDF | RDA |
Life Chemicals has a large collection of ~380,000 diverse small molecule compounds. The entire compeound library may be interrogated one-by-one by experimentation. This would require purchasing the whole stock, which is not a frugal option. Therefore, I have pre-assembled a number of custom collections for specific chemical genetics research subtypes. In addition, the user may assemble a custom collection based on custom filters on using a web application that will be described.
Several lists, see table, are used to search for structurally similar molecules in the Life Chemicals stock. To learn more about the cheminformatics operations please see the folder R/ for executable code to perform various Tanimoto searches based on seed lists.
The following are several lists used to assemble subsets of the Life Chemicals stock:
| Annotation | Seed txt | Seed SDF | Stock TXT | Stock SDF |
|---|---|---|---|---|
| PubChem Bioassay Bioactives | TXT | SDF | TXT | SDF |
| Plant Growth Regulators | TXT | SDF | TXT | SDF |
| Agrochemicals | TXT | SDF | TXT | SDF |
| Pesticides | TXT | SDF | TXT | SDF |
| Herbicides | TXT | SDF | TXT | SDF |
| Theme | Seed txt | Seed SDF | Stock TXT | Stock SDF |
|---|---|---|---|---|
| Author | TXT | SDF | TXT | SDF |
| TXT | SDF | TXT | SDF | |
| Book | TXT | SDF | TXT | SDF |
| Custom | Seed txt | Seed SDF | Stock TXT | Stock SDF |
|---|---|---|---|---|
| Target library via Protein query | ||||
| test with pyr/pyls |
To provide a sample of chemical space the Life Chemicals library has been subset into themed collections based on a seed list containing compounds of interest. Feel free to browse these collections by using the following R Shiny web application.
