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Determining relations between structure and docking quality Bo Hanssen & Sander Jans Supervisor: Prof. dr. Gert Vriend 17-02-2012.

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Presentation on theme: "Determining relations between structure and docking quality Bo Hanssen & Sander Jans Supervisor: Prof. dr. Gert Vriend 17-02-2012."— Presentation transcript:

1 Determining relations between structure and docking quality Bo Hanssen & Sander Jans Supervisor: Prof. dr. Gert Vriend 17-02-2012

2 Outline Introduction Software Self-/crossdocking Experiment Templates Code Results Discussion

3 Introduction Will better structures lead to better docking quality?

4 Software Docking Tools: -AutoDock (4.2) -Fleksy (1.2.2) -FlexX (1.3.0) Calculation Tools: -Yasara/What if twinset (11.4.18) Helper Tools: -Flexor (0.1) -Corina (3.48) Template ‘Tools’: -PDB -PDB_REDO

5 Self Docking Astex Diverse Set 85 proteins and their cocrystallized ligands Cross Docking Set from Nabuurs et al. 21 proteins and their ‘cross’ligands Nabuurs et al. J. Med Chem. 2007, 50, 6507-6518Hartshorn et al. J. Med. Chem. 2007, 50, 726-741

6 Experiment

7 Templates Apo vs. Holo

8 Code

9 Results

10

11 Discussion WHAT_CHECK errors. How to analyze data (PCA?) Flexor not working optimal, ok to edit?

12 Questions?


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