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

Abstract

Background: 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.

Results: We describe a new software toolkit--the Molecular Biology Toolkit (MBT; http://mbt.sdsc.edu)--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.

Conclusions: 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).

Figure 1

The architecture of the toolkit.

Figure 2

The MBT data model.

Figure 3

The class hierarchy of the geometry engine.

Figure 4

Ligand Explorer. The structure of cAMP dependant protein kinase (PDB id 1ATP) showing the hydrophilic interactions of the bound ATP to the protein and bound inhibitor which mimics substrate in the phosphotransfer reaction from the gamma phosphate of ATP.

Figure 5

Protein kinase explorer. An alternative view of a cAMP dependant protein kinase with residues from the multiple structure alignment mapped to the corresponding aligned sequences and to a single template structure from the set.