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Determining relations between structure and docking quality Bo Hanssen & Sander Jans Supervisor: 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 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
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
Templates Apo vs. Holo
Discussion WHAT_CHECK errors. How to analyze data (PCA?) Flexor not working optimal, ok to edit?
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