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Automated determination of interhelical angles for protein alpha helices from coordinate data

This proposed method aims to automate the determination of interhelical angles for protein alpha helices using coordinate data. The results show good agreement with observed values.

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Automated determination of interhelical angles for protein alpha helices from coordinate data

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  1. Automated determination of interhelical angles for proteinalpha helices from coordinate data Robert Fraser, James Stewart, Janice Glasgow Queen's University School of Computing, Kingston, ON

  2. Protein Structure • Contact Maps • Helix Packing Models • Proposed Method • Results

  3. The HUGE picture • Sequence  Structure • Structure  Function • I’m working on a tiny bit of the first step

  4. Protein Structure • Different levels of structure • We’re interested in alpha helices Used with permission from Petsko, G.A. and D. Ringe, Protein Structure and Function, 2004

  5. Contact Maps • Distance map represents full 3D structure • Contact map is a binary version • 10Ǻ threshold used here

  6. Knobs and Holes • Steric surface of the molecule

  7. Two surfaces to a helix

  8. Sign is important

  9. Angle method • if (da× db) ·(b0 – a0) > 0 • then the top vector is rotated clockwise • else the top vector is rotated counter-clockwise • Clockwise  negative sign

  10. Comparison to observed values

  11. Results • 4.1° +/- 3.2° of observed data • 3.6° +/- 1.9° after removing an outlier

  12. Acknowledgements • Kelly Fraser • Janice Glasgow • James Stewart • Henk Meijer • Mehdi Hedjazi • Alan Ableson • Eduardo Zuviria • Tony Kuo

  13. Thank you • Questions?

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