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Software Overview:
The Molecular Biology Toolkit (MBT) is a Java-based protein visualization and analysis system. 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. Also, 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).
The toolkit provides the capability to load molecular data from a number of sources, including files of types PDB, mmCIF, and FASTA. These file types can be read from local disk or from an HTTP or FTP server. This distribution of the MBT provides several StructureLoader implementations to read common data formats, although researchers also can write and register their own custom loaders for the toolkit. Most of the provided StructureLoader implementations also can read from files compressed in the "zip" or "gzip" formats.
The MBT makes possible new methods of interactive visualization of complex scientific data. While most existing methods of representing scientific data are static and two-dimensional, the MBT's visualization capabilities provide interactive, three-dimensional environments within which multiple users can examine complex data sets in real time. The distribution supplies a 3-D structure viewer, a 2-D sequence viewer, and a hierarchical tree viewer; users also can write and plug in their own viewers.
Additional information can be found at http://mbt.sdsc.edu/
Commercial Use:
MBT is available for commercial use under copyright license from The Regents of the University of California.
Case No: SD2004-815
Inquiries To: invent@ucsd.edu
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