Probabilistic Prediction of Contacts in Protein-Ligand Complexes 英文参考文献.docVIP

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Probabilistic Prediction of Contacts in Protein-Ligand Complexes 英文参考文献.doc

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Probabilistic Prediction of Contacts in Protein-Ligand Complexes 英文参考文献

ProbabilisticPredictionofContactsinProtein-Ligand Complexes RikuHakulinen1*,SanteriPuranen2,JukkaV.Lehtonen2,MarkS.Johnson2,JukkaCorander3 1Department of Natural Sciences, Mathematics and Statistics, Abo? Akademi University, Turku, Finland, 2Department of Biosciences, Abo? Akademi University, Turku, Finland,3DepartmentofMathematicsandStatistics,UniversityofHelsinki,Helsinki,Finland Abstract We introduce a statistical method for evaluating atomic level 3D interaction patterns of protein-ligand contacts. Such patterns can be used for fast separation of likely ligand and ligand binding site combinations out of all those that are geometrically possible. The practical purpose of this probabilistic method is for molecular docking and scoring, as an essentialpartofascoringfunction.Probabilitiesofinteractionpatternsarecalculatedconditionalonstructuralx-raydata and predefined chemical classification of molecular fragment types. Spatial coordinates of atoms are modeled using a Bayesian statistical framework with parametric 3D probability densities. The parameters are given distributions a priori, whichprovidesthepossibilitytoupdatethedensitiesofmodelparameterswithnewstructuraldataandusetheparameter estimatestocreateacontacthierarchy.Thecontactpreferencescanbedefinedforanyspatialareaaroundaspecifiedtype offragment.Wecomparedcalculatedcontactpointhierarchieswiththenumberofcontactatomsfoundnearthecontact point in a reference set of x-ray data, and found that these were in general in a close agreement. Additionally, using substratebindingsiteincathechol-O-methyltransferaseand27smallpotentialbindermolecules,itwasdemonstratedthat these probabilities together with auxiliary parameters separate well ligands from decoys (true positive rate 0.75, false positive rate 0). A particularly useful feature of the proposed Bayesian framework is that it also characterizes predictive uncertaintyintermsofprobabilities,whichhaveanintuitiveinterpretationfromtheappliedperspective. Citation:Hak