Protein Data Bank Integrates SDSC Interactive Collaborative Environment

Published 06/04/2001

UNIVERSITY OF CALIFORNIA, SAN DIEGO - The Protein Data Bank (PDB: http://www.pdb.org/) has announced that the Molecular Interactive Collaborative Environment (MICE) developed by the San Diego Supercomputer Center (SDSC) has been integrated with the PDB, allowing teams of scientists worldwide to view and interact simultaneously with 3-D scenes of biological molecules through ordinary Web browsers.

"SDSC's MICE is the first tool that lets scientists view 3-D structures together and interactively, which is a major advance for the PDB," said Philip E. Bourne, Co-Director of the Protein Data Bank (PDB), the world repository for 3-D macromolecular structure data managed by teams at Rutgers University, SDSC, and the National Institute of Standards and Technology. PDB stores the sequences and structures of proteins and contains numerous tools for pinpointing and visualizing the data.

"Using MICE," said SDSC developer John Moreland, "one participant can 'publish' a 3-D molecular scene, and all participants can view it simultaneously with an ordinary Web browser, no matter where they are located." Scientists can share and manipulate entire 3-D molecular structures instead of static two-dimensional snapshots, in real time. A structure can be manipulated on screen and examined from any angle.

Since individual elements of a protein structure and its gross shape can play various roles in molecular interactions, SDSC's MICE is a very useful viewing environment "for examining structures and predicting functional characteristics of large biological molecules like the proteins that carry out most of the body's work," Bourne said. He noted that in the first weeks of availability, about 2,200 accesses to MICE were registered.

"MICE fits perfectly with the PDB's mission of enabling science, and arrives at a time when structures are growing in terms of number and complexity," said Helen M. Berman of Rutgers University, Director of the PDB. "This method of interaction and collaboration will promote new ways of seeing and thinking about structure, and it is a welcome addition to our current suite of tools."

MICE AND ITS FEATURES

MICE was initially developed at SDSC, first as a demonstration presented at the SC96 conference and then under a grant from the National Science Foundation to Bourne. Moreland and John Tate (now of the University of Oxford, UK) were the major developers. Tate, in particular, implemented a Molecular Scene Generator using a framework previously available through the PDB for static image displays. Implementing the complete MICE environment, however, has now enabled interactive collaboration.

To use the MICE environment, a PDB user must identify a molecule and select View Structure from the Structure Explorer menu. MICE is presented as a viewing option, and selecting this link shows the chosen structure in a new window. The basic backbone structure can then be enhanced via a series of dialog boxes that allow scientists to focus on secondary or tertiary structure. A collaborative group can switch control of the molecular scene from one person to another on the fly. Tools for pointing, labeling, and fly-through are also available. New structures can be accessed directly from the MICE windows.

MICE is implemented as a Java applet and requires Sun's Java 2 Runtime Environment (JRE), the corresponding Java plug-in, and a Java3D extension. Instructions are available on the PDB Web site.

The underlying visualization files are generated by MolScript in VRML format. MolScript was developed by Per Kraulis of the Stockholm Bioinformatics Center. The front-end files are manipulated by a series of Java and Java3D scripts, the details of which are hidden from the users. Follow-on work is planned to implement some of the server-side rendering on the client side, making operation faster, and new tools will be added to permit simultaneous access to sequence and structure.

The Protein Data Bank is operated by the Research Collaboratory for Structural Bioinformatics (RCSB; http://www.rcsb.org/) and is supported by funds from the National Science Foundation, The Office of Biological and Environmental Research at the Department of Energy, and two units of the National Institutes of Health: The National Institute of General Medical Sciences and the National Library of Medicine. The RCSB is a consortium consisting of Rutgers University (http://www.rutgers.edu/), San Diego Supercomputer Center (http://www.sdsc.edu/), and The National Institute of Standards and Technology (http://www.nist.gov/). For more information on the PDB or RCSB, please contact info@rcsb.org.

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Contact:
David Hart, SDSC, 858-534-8314, dhart@sdsc.edu