BioCurrents Research Center

Thanks to the following for materials & support

www.pharmabase.org
An open access database of cellular physiology and pharmacology

**Now featured in the cheminformatics section of Current Protocols in Bioinformatics, Section 14.2.2 (John Wiley & Sons, 2006)**

This NIH: NCRR-funded database has been developed by the BioCurrents Research Center (BRC) as a research tool and a resource for scientists and students on the use of pharmacological compounds in cellular research. The database is organized by several categories, such as compound or subject, membrane transport and disease. Information is arranged in a hierarchical manner and can be expanded to view the entire list. Users have the option of navigating by subject or through a graphics interface, with each level linking to a list of related compounds.

Through its heirarchical subject navigator, Pharmabase leads users through a series of choices until they arrive at the desired end point, and each level reveals all related compounds. At any point in the tree the list can be expanded and viewed in its entirety. The search function can also be utilized to reach either subjects or compounds directly.

Pharmabase offers a unique relational graphics navigator tool which allows users to enter the database through an interface of images, beginning with cell types and progressing on to deeper levels of detail, such as structures and transport mechanisms as shown below. Pathway components are linked to lists of related compounds, just as with the subject navigator.


Click on above images to view related pages on Pharmabase.

The compound record is divided into sections: The header bar, the compound or subject search, the navigator and the route window. This includes synonyms and links to gene and structural information. Each record covers the following:

~ Action: Defines the targets of the compound and its effect, for example whether it acts as an inhibitor or agonistic.
~ Preparation: Solubility in a biological rather than a chemical context at concentrations at or above the biological threshold.
~ Thresholds: When available, this gives the final concentrations needed to block the action of a target protein.
~ Comment: Particular features of the compound which need to be emphasized, such as lack of specificity.

Click here for a sample compound record page.

Permission to reproduce some detailed compound information from Calbiochem and BioMol is gratefully acknowledged and to Alomone Labs for the links to their review articles.

Proceed to www.pharmabase.org