Search results for "MM-PBSA"

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Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening.

2015

In drug discovery the reliable prediction of binding free energies is of crucial importance. Methods that combine molecular mechanics force fields with continuum solvent models have become popular because of their high accuracy and relatively good computational efficiency. In this research we studied the performance of molecular mechanics generalized Born surface area (MM-GBSA), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and solvated interaction energy (SIE) both in their virtual screening efficiency and their ability to predict experimentally determined binding affinities for five different protein targets. The protein-ligand complexes were derived with two different app…

molecular mechanics generalized Born surface areaPhosphodiesterase InhibitorsMolecular Dynamics Simulationta3111Molecular mechanicsMolecular Docking Simulationbeta-LactamasesMolecular dynamicssolvated interaction energyBacterial ProteinsComputational chemistryAldehyde ReductaseDrug DiscoveryMaterials ChemistryHumansHSP90 Heat-Shock ProteinsPhysical and Theoretical ChemistryBeta-Lactamase InhibitorsSpectroscopymolecular mechanics Poisson-Boltzmann surface areaMM-GBSAVirtual screeningBinding SitesChemistryPhosphoric Diester Hydrolasesta1182Hydrogen BondingInteraction energyvirtual screeningComputer Graphics and Computer-Aided DesignMolecular Docking SimulationMM-PBSAModels ChemicalROC CurveSolvent modelsDocking (molecular)Area Under CurveBiological systemReceptors Progesteronebeta-Lactamase InhibitorsHydrophobic and Hydrophilic InteractionsProtein BindingJournal of molecular graphicsmodelling
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