A Distributed Protein Visualization Application
  
Protein visualization has become increasingly popular especially since
the accomplishment of the Human Genome Project.  Although there are
several visualization software available for scientists, few address
the aspect of collaboration, e.g.  simultaneous access of the same
protein model.  Most of the current systems are standalone applications
and researches have to share their ideas by exchanging snaphots of the
protein models.

We have developed a distributed protein visualization application, in
which a protein molecule can be viewed synchronously by many users in
different geographical locations.  Our system provides different 3D
representations existing in many of today's protein visualization
systems.  These representations include: backbone model, balls-sticks
model, space-fill model, and ribbon model.  The structure information
of protein molecules is obtained in the form of a Protein Data Bank
(PDB) file.  The 3D models are built as Java3D scene graphs using the
atomic coordinate information contained in the PDB file.  User can
interact with the 3D models using zoom, pan and rotation functions.
Furthermore we provide textual information in terms of a "molecule
information window" and a "tree view window".  The former includes
information such as molecule name, number of amino acids in the
molecule, the amino acid chain as one-letter symbols, and currently
selected amino acid. The latter describes the hiearchy of the protein
molecule both in terms of primary structure and the secondary
structure.  We implemented two way interaction between the hiearchical
representation and the 3D models in the following sense.  Users can
select a sub-structure, e.g. an amino acid or an atom, in the molecule
using either the tree view or the 3D view, and the corresponding
structure is highlighted in the other view.

A session server handles the communication between the users.  Users
share the same view of a 3D protein model by using a locking mechanism.
Our implementation is based on Java. It allows users from different
platforms connect to the same collaboration session.

We plan to add new 3D representations,such as electron density map and
solid surface model, into our visualization system.  We also consider
incorporating a protein folding algorithm, which will enable users not
only visualize proteins of unknown structure, but also model and create
new proteins on the fly by changing the amino acid sequence.