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

We describe a new software toolkit – the Molecular Biology Toolkit (MBT; http://mbt.sdsc.edu 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).Recent scientific and technical advances in the field of experimental biology, particularly in genomics, have produced large amounts of biological data, which has posed new conceptual challenges. The visualization and visualization-driven analysis of these experimentally derived data has become a key component of the scientific process.Until recently, these needs were typically approached by designing applications specialized in a set of well-defined specific tasks. So, for example, popular applications for molecular visualization include, but are not limited to, Molscript [1], PyMol [2], Rasmol [3] and Swiss-PdbViewer [4]. However, the analysis of these molecular data frequently requires novel approaches to visualization and integration with a variety of data types. Therefore, the ability to quickly prototype and develop software suitable for diverse tasks becomes paramount. Hence, libraries, like the MBT described here, are particularly useful, especially given that many applications can be accessed through the Web.This paper, aimed at bioinformatics software developers, provides a concise presentation of the design and capabilities of the toolkit, presents a number of models for its usage, and illustrates its perf