Determining relations between structure quality and docking quality

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

06-04-2012

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

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

Data• Outliers via Grubbs’ Test• Centre of Mass

Results

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

Further research

Hartshorn et al. J. Med. Chem. 2007, 50, 726-741

• 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

Questions?