Using Pharmabase to Perform Pharmacological Analyses of Cell Function

Peter J. S. Smith1, David Remsen1

1 BioCurrents Research Center, Marine Biological Laboratory, Woods Hole, Massachusetts
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 14.2
DOI:  10.1002/0471250953.bi1402s13
Online Posting Date:  March, 2006
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Pharmabase is designed to form a bridge between the molecular dimension of cell transport processes and the functional manipulation of the protein players. It has as its emphasis membrane transport and related pharmacology. Several search and navigation options are available, including membrane transport, disease, and a graphic interface arranged by pathway and cell type. The level of entry to the database can be tailored to the investigator's level of expertise. The final product of Pharmabase is a Compound Record detailing the use and targets of individual compounds. Navigation routes generally fall into hierarchical keys and are cross‐referenced. Pharmabase encourages input from its user community. It is maintained by the BioCurrents Research Center, an NIH resource funded through the National Center for Research Resources (NCRR).

Keywords: Pharmacology; Channels; Pumps; Carriers; Protein transporters

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Table of Contents

  • Basic Protocol 1: Navigating the Home Page of Pharmabase Using Compound and Subject Search
  • Basic Protocol 2: Using the Subject Navigator: Membrane Transport
  • Basic Protocol 3: Searching Pharmabase by Biochemical Pathway or Cell Structure Targets
  • Basic Protocol 4: Using the Graphic Navigator: Searching Cell Type or Pathway
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

   Barchan, D., Kachalsky, S., Neumann, D., Vogel, Z., Ovadia, M., Kochva, E., and Fuchs, S. 1992. How the mongoose can fight the snake: The binding site of the mongoose acetylcholine receptor. Proc. Natl. Acad. Sci. U.S.A. 89:7717‐7721.
   Greenberg, R.M. 2005. Are Ca2+ channels targets of praziquantel action? Int. J. Parasitol. 35:1‐9.
   McDonough, S.I. 2003. Peptide toxin inhibition of voltage gated calcium channels: Selectivity and mechanisms. In Calcium Channel Pharmacology, 1st ed. (S.I. McDonough, ed.). Plenum, New York.
   Rose, M.R. and Griggs, R.C. 2001. Channelopathies of the Nervous System, p. 347. Butterworth‐Heinemann, Burlington, Mass.
Internet Resources
Key References
   Ashcroft, F.M. 2000. Ion Channels and Disease. Academic Press, Inc., San Diego, Ca.
  A text that covers channels, receptors, and gap junctions, as related to disease.
   Hille, B. 2001. Ion Channels of Excitable Membranes. Sinauer Associates, Inc., Sunderland, Mass.
  An advanced biophysical text that covers channel properties in excitable cells.
   Piccolino, M. 1997. Luigi Galvani and animal electricity: Two centuries after the foundation of electrophysiology. Trends Neurosci. 20:443‐448.
  A general introduction, from an historical perspective, to excitable membranes.
   Stein, W.D. 1990. Channels, Carriers, and Pumps. Academic Press, Inc., San Diego, Ca.
  Although now dated, this is an excellent and well written introduction to the field of transmembrane transport mechanisms.
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