E-MSD: an integrated data resource for bioinformatics.

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).

Design and implementation of a collaborative molecular graphics environment.

During the determination of macromolecular structures, scientists routinely use complex graphics software to display various representations of the molecule of interest. Once the structure determination is complete, coordinates are deposited in the Protein Data Bank (PDB), from where anyone with an Internet connection may download and view them or request them on CD-ROM. However, the currently available visualization software is such that causal users, whose expertise may not be in structure determination, often cannot obtain useful images of interesting molecules without expending considerable time and effort. Existing visualization software is generally very complex, requiring a high degree of familiarity to obtain the best results, or else it is too simplistic to provide users with the level of customizability needed to get the most out of the atomic coordinates. Few of the existing software packages have the capability for collaborative visualization via the Internet. These and other issuses are being addressed by the Molecular Interactive Collaborative Environment (MICE) project (http://mice.sdsc.edu/). The core of the MICE project is the MICE application, an interactive molecular structure viewer with built-in collaborative capabilities. MICE not only addresses the issues of usability and flexibility but also extends the role of traditional visualization tools by allowing multiple users to view, manipulate, and interact with a single representation of a macromolecular structure. MICE is written entirely in Java, using the Java3D extensions for rendering and manipulation of the three-dimensional scene, and the Common Object Request Broker Architecture (CORBA) communications suite to enable collaborative manipulation of that scene.