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

Searching for Substance info

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


momeara/Zr documentation built on Jan. 11, 2022, 8:11 a.m.