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Advanced Imaging Magazine

Updated: July 8th, 2008 05:26 PM CDT

Navigating Around the Building Blocks of Life

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FEATURE STORY

Navigating Around the Building Blocks of Life

Visualizing the 3D structures of macromolecules at atomic resolution—an important application in biotechnology and the biosciences...

by Karsten Fries and Seán I. O'Donoghue

September 2002

protein-DNA complex
protein-DNA complex Figure 1 (above left & right)): Two protein-DNA complexes [in yellow) bound along with eight protein molecules. At left, a line connects each bonded pair. At right, a ribbon represents the trace of the polymer backbone in each molecule. The illustrated complex is the nucleosome core particle, a fundamental structure element involved in organizing DNA into chromosomes. Figure 2 (left): Interfacing SRS 3D & the system hardware.

Two main types of macromolecule are proteins and DNA or RNA; both are essentially polymer molecules made of a linear sequence of either amino acids or nucleic acids, respectively (see Figure 1). A typical macromolecular structure consists of around 3,000 atoms, although much larger structures are becoming increasingly available.

There are many systems used to visualize macromolecular structures. However, most are usually stand-alone programs and have some limitations. Most are not integrated together with a system enabling users to easily find the most relevant structure for a given problem. Furthermore, most visualization systems do not take advantage of other related data that can help understand and interpret macromolecular structures. Finally, most systems have been designed more for expert users and emphasize features rather than usability.

To address these shortcomings, we built SRS 3D as an extension to SRS1 (Sequence Wetrieval System), a well-known system for integrating together bioscience databases. SRS 3D makes it easy for bioscientists to find relevant structures, and can integrate data from other feature databases to annotate structures. SRS 3D also includes a new visualization system specifically designed to emphasize usability. Here, we describe some novel features of the SRS 3D Viewer.

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