SUPPLEMENTARY MATERIAL

J. Reichert, A, Jabs, P. Slickers, J. Sühnel,
The IMB Jena Image Library of Biological Macromolecules,
Nucleic Acids Research (in press) - 2000 NAR Biological Database Issue

• Entry page with automatically generated information only
• Entry page with additional manually generated information
• Access modes
• Helix and bending analysis of nucleic acid duplex structures
• The Base Pair Directory
• The Amino Acid Repository

Helix and bending analysis of nucleic acid duplex structures

The Image Library includes a tool for the quantitative analysis of helix and bending properties of approximately 750 nucleic acid double helix structures (free or bound to drugs or proteins). It offers both numerical and visual information on the helix geometry. As shown in Figure 3 for a nucleic acid-protein complex the orientation of the nucleic acid part is not just taken from the PDB or NDB file. Rather, the coordinate axes are aligned to the principal axes of inertia of the helix axis. In this manner the bending features of the nucleic acid helix are clearly shown.

Figure 3. Three orthogonal views of the nucleic acid part of the complex of human TATA-binding protein with TATA-sequence DNA (PDB code: 1tgh, NDB code: pdt024).

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The helical axis is determined with the CURVES algorithm and subsequently the following geometrical models are fitted to this axis: a straight line, a circular line (arc), a kinked line, and a double kinked line. By means of a goodness-of-fit criterion the most appropriate model is selected. This information and the geometrical parameters of the corresponding models (radius of curvature, kink and twist angle) lead to a comprehensive bending classification. In Figure 4 representative examples for the different bending types are shown.

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