Molecular Biotechnology

, Volume 34, Issue 1, pp 69–93 | Cite as

Cataloging the relationships between proteins

A review of interaction databases
  • Carol Rohl
  • Yancey Price
  • Tiffany B. Fischer
  • Milissa Paczkowski
  • Michael F. Zettel
  • Jerry Tsai
Review

Abstract

By organizing and making widely accessible the increasing amounts of data from high-throughput analyses, protein interaction databases have become an integral resource for the biological community in relating sequence data with higher-order function. To provide a sense of the use and applicability of these databases, we describe each of the major comprehensive interaction databases as well as some of the more specialized ones. Content description, search/browse functionalities, and data presentation are discussed. A succinct explanation of database contents helps the user quickly identify whether the database contains applicable information to their research interest. Broad levels of search/browse functions as well as descriptions/examples allow users to quickly find and access pertinent data. At this point, clear presentation of search results as well as the primary content is necessary. Many databases display information graphically or divided into smaller digestible parts over a number of tabbed/linked pages. In addition, cross-linking between the databases promotes interconnectivity of the data and is an added layer of relational data for the user. Overall, although these protein interaction databases are under continual improvement, their current state shows that much time and effort has gone into organizing and presenting these large sets of data-describing protein interactions.

Index Entries

Biological databases protein interactions protein pathways proteomics 

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Copyright information

© Humana Press Inc 2006

Authors and Affiliations

  • Carol Rohl
    • 1
  • Yancey Price
    • 2
  • Tiffany B. Fischer
    • 2
  • Milissa Paczkowski
    • 3
  • Michael F. Zettel
    • 4
  • Jerry Tsai
    • 2
  1. 1.Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck & Co., Inc.Seattle
  2. 2.Department of Biochemistry & Biophysics, Biochemistry/Biophysics Building, 2128 TAMUTexas A&M UniversityCollege Station
  3. 3.Department of Animal SciencePurdue UniversityWest Lafayette
  4. 4.Department of ChemistryCornell UniversityIthaca

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