This vignette describes several use cases for retrieving substance information from zinc15.docking.org using the Zr
R package.
To follow along, make sure Zr package is installed
install.packages("devtools") devtools::install_github("MaomLab/Zr")
And familiarize yourself with with http://zinc15.docking.org
Tanaka et al., (2015, 10.1371/journal.pone.0135657) observe uremic solutes that accumulate when the kidneys fail. In Supplementary table 2, they list the 120 uremic compounds they observe. Here are the ones with HMDB Ids:
uremic_solutes <- c("HMDB00001", "HMDB00017", "HMDB00020")
To retrieve information about these compounds we can use Zr
package
library(Zr) library(dplyr) s_info <- search_for_substances(uremic_solutes, verbose=T) s_info %>% str
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