UCT CS Research Document Archive

DOCKside II: Adding Functionality to Current Molecular Docking System

Campbell, Dumisani, Johannes Jansen van Vuuren and Ian Kitley (2006) DOCKside II: Adding Functionality to Current Molecular Docking System. Technical Report CS06-12-00, Department of Computer Science, University of Cape Town.

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Abstract

The DOCKside program makes use of Electron Microscopy (EM) maps and X-Ray Crystallography (XRC) maps to dock molecules. This can be achieved either manually or automatically. The automated functions include rigid- and flexible- docking functions. A solution space viewer was also designed to enable users to view the complete solution space that is generated by the automated docking feature of DOCKside.

Testing revealed that the rigid docking procedures of DOCKside, especially Vector Quantization (VQ) performs just as well as the leading docking software packages like Situs. It was further revealed that the visualization tool was successful in conveying seven-dimensional data in an intuitive manner using three-dimensional graphics such as glyphs and starmaps.

In pursuit of a novel flexible docking method, boundary constraints on a simple model, such as a sphere, were investigated. Successful simulations were obtained where external forces acted upon the molecular structure pushing it back into the boundary constraints.

EPrint Type:Departmental Technical Report
Subjects:I Computing Methodologies: I.2 ARTIFICIAL INTELLIGENCE
I Computing Methodologies: I.3 COMPUTER GRAPHICS
I Computing Methodologies: I.6 SIMULATION AND MODELING
ID Code:355
Deposited By:Jansen van Vuuren w, J
Deposited On:13 November 2006