[Molvis-list] Molecular Biology Toolkit - building a community

John Beaver jbeaver at sdsc.edu
Thu Oct 5 15:57:35 EDT 2006

We are seeking to build a developer community around the Molecular
Biology Toolkit. Unfortunately, I have no experience with this. Does
anyone have suggestions (i.e., mailing lists, forums)? Does anyone have
opinions on the need for such a community?




The Molecular Biology Toolkit (http://mbt.sdsc.edu
<http://mbt.sdsc.edu/> )* is a powerful Java toolkit for creating
applications which utilize structural protein data. It offers clean data
structures and (optional) visualization using the latest graphics



It is used as a basis for three visualization tools (more on the way)
developed by the San Diego Supercomputer Center for use on the RCSB PDB
(www.pdb.org <http://www.pdb.org/> ) and Immune Epitope Database
(www.immuneepitope.org <http://www.immuneepitope.org/> ), as well as
internally by the PDB website. The viewers include:

-          ProteinWorkshop (www.pdb.org): intended as a tool for
creating publication quality images of proteins

-          EpitopeViewer (www.immuneepitope.org
<http://www.immuneepitope.org/> ): allows the viewing of
receptor-antigen structures, incorporating data from the Immune Epitope

-          Ligand Explorer (www.pdb.org <http://www.pdb.org/> ): allows
the viewing of 


Current status:

-          Since the visualization component is new, we are currently
integrating new representations. Currently, we are working on adding
water-accessible surface rendering, and we expect it to be finished
within the next four to five months.



>From the MBT website, "Permission to use, copy, modify and distribute
any part of the Molecular Biology Toolkit (MBT) for educational,
research and non-profit purposes, without fee, and without a written
agreement, " provided they display the copyright. Commercial users would
need to contact the University of California.



* The version of the MBT on the web site is old, and we can provide a
newer version to those interested. An official 2.0 release of the MBT,
with an incredible number of improvements will be available soon.

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