Scientists worldwide can share molecular scenes in a collaborative environment

San Diego 12 June 2001The Molecular Interactive Collaborative Environment (MICE) developed by the San Diego Supercomputer Center (SDSC) has been integrated with the Protein Data Bank (PDB), allowing teams of scientists worldwide to view and interact simultaneously with 3D scenes of biological molecules through ordinary Web browsers. This method of interaction and collaboration will promote new ways of seeing and thinking about structure, and is a welcome addition to the current suite of tools, according to Helen M. Berman of Rutgers University, Director of the PDB.

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

"Using MICE", explained SDSC developer John Moreland, "one participant can publish a 3D 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 3D 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", Mr. Bourne stated. He noted that in the first weeks of availability, about 2200 accesses to MICE were registered.

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 Mr. Bourne. John Moreland and John Tate, now at the University of Oxford in the United Kingdom, were the major developers. John 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 dialogue boxes which 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, labelling, 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 visualisation files are generated by MolScript in VRML (Virtual Reality Modelling Language) 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) 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 which are the National Institute of General Medical Sciences and the National Library of Medicine. The RCSB is a consortium consisting of Rutgers University, San Diego Supercomputer Center, and the National Institute of Standards and Technology. For more information on the Protein Data Bank, you can contact the Research Collaboratory for Structural Bioinformatics.


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