The Molecular Biology Toolkit (MBT) is a Java-based protein visualization and analysis toolkit. The toolkit provides classes for efficiently loading, managing and manipulating protein structure and sequence data. The MBT also provides a rich set of graphical 3D and 2D visualization components which can be easily "plugged together" to produce applications having sophisticated graphical user interfaces. Yet, with all of the GUI components provided in the toolkit, the core data i/o and manipulation classes may be used to write completely non-graphical applications (say, for implementing pure analysis codes, or, for producing a non-graphical "back end" for web-based applications).

There are a large number of very powerful and popular stand-alone applications for the visualization and analysis of protein data. Be sure that we have no intention to reproduce their functionality in order to compete head-to-head with those applications. But, when we began the MBT project there were few if any well documented and easy to use developer's toolkits to enable the creation of custom molecular biology visualization and analysis applications.

With many major biological research resources being deployed via the web, none of the toolkits enabled applications themselves to be easily deployable both as stand-alone applications OR directly through a web interface. Even fewer packages enabled applications to run seamlessly on multiple computer platforms.

Since this project was undertaken as a "companion" project to the Protein Data Bank project, we had the additional desire to create a toolkit which could ultimately integrate seamlessly with that resource. One of our goals is to enable the transparent network access of protein data from the PDB site as well as interactive database query capability into the PDB site. For example, imagine being able to select a 3D structure in an MBT application and then be able to select a menu to find other similar structures in the PDB database.