Using ChemBank to Probe Chemical Biology

Kathleen Petri Seiler1, Heidi Kuehn1, Mary Pat Happ1, Dave DeCaprio1, Paul A. Clemons1

1 Chemical Biology Program and Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 14.5
DOI:  10.1002/0471250953.bi1405s22
Online Posting Date:  June, 2008
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ChemBank ( is a public, Web‐based informatics environment. ChemBank stores and makes freely available data derived from small molecules and small‐molecule screens and has resources for relating and studying these data. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays performed at the Broad Institute screening center. Web‐based analysis tools are available within ChemBank to study the relationships between small molecules, cell measurements, and cell states. This unit demonstrates the use of ChemBank data to ask and answer questions relating to chemical biology and screening experiments contained within ChemBank. Curr. Protoc. Bioinform. 22:14.5.1–14.5.26. © 2008 by John Wiley & Sons, Inc.

Keywords: chemical biology; cheminformatics; data analysis; database; high‐throughput screening; small molecule

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Table of Contents

  • Introduction
  • Basic Protocol 1: Make a Hypothesis about the Potential Biological Activity of a Molecule
  • Basic Protocol 2: Select Tested Compounds on Which to Pursue Additional Screening or Follow‐Up Chemistry
  • Basic Protocol 3: Determine Which Small Molecules May Perturb Biological Pathways and Processes
  • Basic Protocol 4: Dissect Small‐Molecule Structure Using Assay Profiles
  • Basic Protocol 5: Identify Structurally Related Small Molecules with Known Biological Functions
  • Basic Protocol 6: Download Data for Further Calculation Using External Applications
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

Literature Cited
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