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Distributed PDB Users Can Share 3D Images Using New Interactive Environment from SDSC

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Users of the Protein Data Bank have access to a new tool that will allow them to interact simultaneously while viewing 3D protein structures.

The Molecular Interactive Collaborative Environment (MICE) developed by the San Diego Supercomputer Center has been integrated with the PDB www.pdb.org as a new viewing option. A PDB user first identifies a molecule and then selects View Structure from the Structure Explorer menu. Several distributed users can switch control of the molecular scene from one person to another as needed, using tools for pointing and labeling to collaborate on a single molecule.

The interactive capability provided by MICE “is a major advance for the PDB,” said Philip Bourne, co-director of the PDB, which is managed by the Research Collaboratory for Structural Bioinformatics and run by teams at Rutgers University, SDSC, and the National Institute of Standards and Technology.

Using MICE, one participant at a time acts as the “publisher” for a 3D molecular scene, allowing him or her to manipulate and query the molecule in real time, while other participants can view it simultaneously with an ordinary Web browser as “subscribers.” Participants can switch roles between publisher and subscriber to highlight different features of interest.

MICE is implemented as a Java applet and requires Sun’s Java 2 Runtime Environment, the corresponding Java plug-in, and a Java3D extension, which are freely available from the PDB website. The underlying visualization files are generated by MolScript in VRML (virtual reality modeling language) format. Bourne said the SDSC plans to replace the viewing portion with a new “molecular biology toolkit” that will capture other forms of data besides structure, including sequence, genomic data, and active sites. The new front end is planned for release in a year.

MICE was developed under a $450,000 grant from the National Science Foundation.

Bourne said that about 2,200 PDB users have registered to access MICE so far.

— BT

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