determining relations between structure quality and docking quality
DESCRIPTION
Determining relations between structure quality and docking quality. Bo Hanssen & Sander Jans Supervisor: Prof. dr. Gert Vriend. 06-04-2012. Outline. Introduction Software Self-/crossdocking Experiment Templates Data Results Further research. Introduction. - PowerPoint PPT PresentationTRANSCRIPT
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?