Determining relations between structure and docking quality

Bo Hanssen & Sander JansSupervisor: Prof. dr. Gert Vriend

17-02-2012

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

Introduction• Will better structures lead to better docking quality?

Software

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

Experiment

Templates• Apo vs. Holo

Code

Results

Results

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

Questions?