Helices found by geometric hashing

Nina Amenta, Sunghee Choi, Maria Jump, Ravi Kolluri, Thomas Wahl


We compute our triangulated skeleton, the `power-shape', of an iso-surface in an electron density map. The vertices of the triangles are points that might lie near the molecular backbone. Alpha-helices show up visually as highly interconnected regions of the power shape. The image above is the power-shape of a 3-Angstrom resolution density map of the yMTD protein, given to us by Prof. Jon Robertus.

Using a computer vision technique called geometric hashing (with some speed-ups enabled by the structure in the power shape), we label the points which lie in helical sub-structures. On this example, the process succeeds in finding the longer helices in the reconstructed model, from the density data alone. A small helix (six amino acids) is not found. All of the helical points seem to belong to genuine helices.



The white line is the molecular backbone from Prof. Robertus' reconstruction of the molecule, included to show that we are indeed finding the helicies. The magenta helix points far from the molecular backbone are helices in the density map but outside the molecule (parts of other copies of the molecule in the crystal). Here's another view.



Since our skeleton is easy to map back to the iso-surface, we can label the parts of the iso-surface belonging to helices.



Here are the helices alone, with the backbone for reference.

Nina Amenta
Last modified: Sat Jan 27 12:57:50 CST 2001