drugTargetInteractions

Workflows

Standard Workflow

Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database. ChEMBL has been chosen for this purpose, because it provides one of the most comprehensive and best annotatated knowledge resources for drug-target information available in the public domain.

library(drugTargetInteractions)
chembldb <- system.file("extdata", "chembl_sample.db", package="drugTargetInteractions")
resultsPath <- system.file("extdata", "results", package="drugTargetInteractions")
config <- genConfig(chemblDbPath=chembldb, resultsPath=resultsPath)
downloadUniChem(config=config)
cmpIdMapping(config=config)
queryBy <- list(molType="cmp", idType="chembl_id", ids=c("CHEMBL17", "CHEMBL19"))
qresult1 <- drugTargetAnnot(queryBy, config=config)

Input: A list containing query molecule/protein IDs and a configuration object. Output: A data.frame of drug-target annotations.

When to Use

• Identify drug-target interactions for sets of small molecules or gene/protein identifiers using a local SQLite instance of the ChEMBL database.
• Retrieve UniProt IDs for Ensembl gene IDs using sequence similarity nearest neighbors (SSNNs) via getUniprotIDs or paralogs via getParalogs.
• Query bioactivity data for compounds or proteins using drugTargetBioactivity.

When NOT to Use

• For high-throughput de novo molecular docking or 3D structure-based drug design, use packages like Rcpi or external tools.
• For querying online databases directly without a local SQLite copy of ChEMBL, use direct web API clients.