DOCKside II: Adding Functionality to Current Molecular Docking System

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

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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.

Item Type: Technical report
Subjects: Computing methodologies > Artificial intelligence
Computing methodologies > Computer graphics
Computing methodologies > Modeling and simulation
Date Deposited: 13 Nov 2006
Last Modified: 10 Oct 2019 15:35

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