Determining relations between structure quality and docking quality

1. Determining relations between structure quality and docking quality Bo Hanssen & Sander Jans Supervisor: Prof. dr. GertVriend 06-04-2012

2. Outline • Introduction • Software • Self-/crossdocking • Experiment • Templates • Data • Results • Further research

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

6. Experiment

7. Templates • Apo vs. Holo

8. Data • Outliers via Grubbs’ Test • Centre of Mass

9. Results • Autodock Emin, no flexibility • Structure quality not limiting factor in docking • High σ

10. Further research • First of all: poster • Differences in performance of docking tools • For starters: these 4 classes Phylogenetic tree of protein similarity in the Astex Diverse Set Hartshorn et al. J. Med. Chem.2007, 50, 726-741

11. Questions?