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New Database Provides Quick Window into Protein-Protein Interaction
  
By Sarah Lesher

A new online database enables biologists to tap into annotated entries on the 3,000 most-studied human proteins and how they interact. Protein-protein interactions are increasingly viewed as fundamental to understanding the dynamics of human health and disease.

The Human Protein Reference Database (HPRD) was compiled by principal investigator Akhilesh Pandey, of Johns Hopkins University Medical School in Baltimore, Maryland, and a team of colleagues, most of whom are biologists at the Institute of Bioinformatics in Bangalore, India . Pandey also serves as the chief scientific advisor of the bioinformatics center.

At least 70 databases include information on various aspects of protein–protein and protein-gene interactions. Pandey perceived a need for a single database of searchable, cross-linked information. Rather than cobbling the existing databases together, he enlisted software engineers to design a structure that permits searches by protein name, molecular class, size, localization and functions, modifications that occur in the protein, and a range of other characteristics. Each datum is referenced to the experimental literature.

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Human Protein Reference Database

The compilers searched more than 300,000 articles on PubMed, the U.S. National Library of Medicine's digital archive of life sciences journal literature. Pandey expects that the database will hold comprehensive information on 10,000 human proteins by the year's end.

Now, the database presents more than 10,000 annotated direct protein-protein interactions that the compilers gleaned from published reports of individual small-scale experiments.

In an article in Genome Research, the authors explain that they hope their work will “make it easier to establish a benchmark database for human proteins.”

Database access is free to academic researchers. Companies interested in using the database will pay fees according to licensing criteria being established by Johns Hopkins Licensing and Technology Development.

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Peri, Suraj et.al. Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans. Genome Research 13, 2263-2371. (October 2003).

 

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