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The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications

John L Moreland1, Apostol Gramada1, Oleksandr V Buzko1, Qing Zhang1 and Philip E Bourne12*

Author Affiliations

1 San Diego Supercomputer Center, 9500 Gilman Drive, La Jolla, CA 92093, USA

2 Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA

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BMC Bioinformatics 2005, 6:21  doi:10.1186/1471-2105-6-21

Published: 6 February 2005



The large amount of data that are currently produced in the biological sciences can no longer be explored and visualized efficiently with traditional, specialized software. Instead, new capabilities are needed that offer flexibility, rapid application development and deployment as standalone applications or available through the Web.


We describe a new software toolkit – the Molecular Biology Toolkit (MBT; webcite) – that enables fast development of applications for protein analysis and visualization. The toolkit is written in Java, thus offering platform-independence and Internet delivery capabilities. Several applications of the toolkit are introduced to illustrate the functionality that can be achieved.


The MBT provides a well-organized assortment of core classes that provide a uniform data model for the description of biological structures and automate most common tasks associated with the development of applications in the molecular sciences (data loading, derivation of typical structural information, visualization of sequence and standard structural entities).