Extending Data Integration to 3D Molecular Structures

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Extending Data Integration to 3D Molecular Structures

LION bioscience AG has extended SRS data integration to 3D structures. SRS 3D has used Java 3D technology to create state- of- the- art software for the Life Science Industry. Designed for the biochemist or molecular biologist, SRS 3D enables the user to quickly and easily access sequence, structure and feature data from in- house and public databases. SRS 3D is a showcase for not only for Sun's Java technology, but also for LION's data integration platform, SRS.

About LION AG

To accelerate Life Science research and development, LION provides IT products and integrated software solutions within our Life Science Informatics business, LSI, to turn data into information, as well as information into knowledge. These systems and solutions enable our customers to evaluate scientific data more quickly, more effectively and more comprehensively.

SRS 3D

SRS 3D is a module of LION's popular integration software SRS. With SRS 3D, all relevant structural data for a given target sequence can be easily and rapidly retrieved. The appropriate structures can be selected, and visualized together with features and annotations from other databases.

SRS 3D Key Features:

• Finds the most relevant structures quickly and easily
• Pre- calculated database of sequence-to-structure alignments
• Concise graphical summary shows all related structural information for a given sequence
• Extensible system for integrating public and in-house sequence, structure and feature data
• Runs securely behind a firewall
• Intuitive and user-friendly 3D viewer with standard molecular graphics functions and coloring and representations
• Unique features of the 3D viewer include flexible selection, auto-zoom, keyboard navigation, saving/restoring of view state
• Predefined styles and sequence features
• Sequence features can be extracted from other databases on-the-fly and mapped onto structures
• 3D viewer facilitates direct linking from parts of the 3D structure to feature databases ('3D mark-up'), from which feature details can be retrieved
• Advanced querying of structural databases and cross querying to other databases
• Specialist scientific applications to assist in drug target identification (see: www.lionbioscience.com)

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LION's Use of Java 3D

Integral to SRS 3D is Java 3D. Java 3D enabled LION to meet our use-case driven performance requirements, by taking advantage of the latest hardware accelerated technology. Java 3D was selected for the reasons below to develop LION's highly visual tool.

• Ease of Use
  With Java 3D it is easy to generate rudimentary graphical representations. The mature application programming interface (api) was of benefit to us. We were able to steadily redefine our requirements towards a higher quality of visualization within the SRS 3D product development timelines.
• Platform-Independence
  Platform-Independence is a mandatory requirement for every product at LION. We realized that we have found a way to evade hurdles like a decision for OpenGL, DirectX or for another native visualization API. During the QA (Quality Assurance) cycles of SRS 3D we found that the Java technology not only worked for all our currently supported platforms, but even more OS/Hardware combinations.
• Integration
  The opportunity to provide Java 3D based technology as a web-based application (i.e. as a Java Applet) was the main driving force that led LION to use the Java 3D API in SRS 3D development.
• Performance
  SRS 3D has high requirements concerning scalability and performance to the underlying visualization API. Java 3D enabled LION to meet our use-case driven performance requirements, by taking advantage of the latest hardware accelerated technology.

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Figure Captions:

1. Example for the high-quality visualization depicting the structure PDB:1aoi. All geometry is selectable and selection is propagated in between the components of the SRS 3D Viewer.
2. Navigating into the data is easy with the Mouse and/or Key controls. Modify the selection via tabbing through the repspective hierarchy levels of the underlying data and zoom into the parts of interest
3. The SRS 3D Viewer provides you with a state-of-the-art capabilities of a molecular viewer and much, much more. E.g. the accessible surface of the ligand's proximity can easily be computed with 3 clicks.
4. Visualize structure to sequence alignments together with sequence annotation with a single application. Activate annotations on-the-fly and see how they map onto the 3D structure. The SRS 3D Viewer additionally provides linking from annotation data (3D-markup) to the originating databases.