UCT CS Research Document Archive

DOCKside - A Tool for Docking Atomic Molecular Structures into Low-Resolution Electron Microscopy Graphs

Snowden, Andrew, Guy Stern, Michelle Kuttel and James Gain (2005) DOCKside - A Tool for Docking Atomic Molecular Structures into Low-Resolution Electron Microscopy Graphs. Technical Report CS05-08-00, Department of Computer Science, University of Cape Town.

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Abstract

The process of cryo-electron microscopy allows scientists to view the complex structures of
proteins as they bind and interact with one another. This process however, outputs low
resolution noisy density maps which in their initial form are of little use. Through a process called docking, high resolution models of each of the interacting components can be fitted into these low resolution maps so that further study can occur.

DOCKside allows users to interact with 3D representations of the proteins and of the electron density maps. Design was an initial concern. Related work was studied to better create a efficient solution to the problem. Different techniques for visualising the various components are implemented and discussed. Docking can also be performed manually using interactive graphics or automatically using a range of mathematically intensive algorithms. These too are detailed and discussed. Through user testing, a review is made as to how efficient the docking process is in producing meaningful and accurate data when
compared to the automatically docked solutions.

EPrint Type:Departmental Technical Report
Keywords:molecular docking atom PDB spider contour laplacian marching cubes fast fourier transform correlation density
Subjects:J Computer Applications: J.3 LIFE AND MEDICAL SCIENCES
ID Code:247
Deposited By:Snowden, Andrew
Deposited On:21 October 2005