Scientists worldwide can share molecular scenes in a collaborative environmentSan Diego 12 June 2001 The Molecular Interactive Collaborative Environment (MICE) developed by the San Diego Supercomputer Center (SDSC) has been integrated with the e Protein Data Bank (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 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. 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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