Cheminformatic analysis of high-throughput compound screens

Methods Mol Biol. 2014;1056:145-57. doi: 10.1007/978-1-62703-592-7_15.


This article gives an overview of basic computational methods that are commonly used for analyzing small molecule screening data in the chemical genomics field. First, we introduce cheminformatic concepts for analyzing drug-like small molecule structures and their properties. Second, we introduce compound selection approaches for assembling screening libraries using compound property and diversity analyses. Finally, we discuss methods for interpreting screening hits by analyzing compound structures and induced phenotypes using similarity search and clustering approaches. These are critical steps for optimizing screening hits, and relating structure to bioactivity and phenotype.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cluster Analysis
  • Drug Evaluation, Preclinical
  • High-Throughput Screening Assays*
  • Informatics
  • Phenotype
  • Quantitative Structure-Activity Relationship
  • Small Molecule Libraries


  • Small Molecule Libraries