Drug Docking Capstone Class

Projects

• Data Mining
• Kegg Extraction & Manipulation
• Biological Network Simulation
• Drug Docking
• Kegg Schema by Drew (Updated 2007-Feb-14)
• Pathways
• This chapter shows how the RMSD is calculated and how tertiary alignment can be performed.
• Surfaces Alignment Demo (12MB) - Two identical shapes are translated to the origin, and one is rotated until aligned with the other.
• Simple 3D Shape Alignment (1.3MB) - Two identical shapes are translated to the origin, and one is rotated until perfectly aligned with the other (RMSD = 0.000).
• Drugdocking Algorithm Demo (3MB) - The same algorithm is modified for drug docking by translating the molecules within the range of their average diameters and spinning the drug as it creeps along the approximate surface of the protein.
• Biotin docking to Streptavidin Demo (1.6MB) - Animation of a drug docking to a protein after optimal location and rotation are discovered by the algorithm.
• DrugDocking.ppt - PowerPoint presentation given at the Spring 2007 Research Conference
• Pathways
1. I just received this summary of use cases for the pathway database along with a bunch of sources for possible data.
2. This paper discusses some of the methodology in finding this kind of information. Lets read it for next week (2/7/07).