The influence of model building schemes and molecular dynamics sampling on QM-cluster models: the chorismate mutase case study
Donatus A. Agbaglo, Thomas J. Summers, Qianyi Cheng, Nathan J. DeYonker
Abstract
those from MD frames. The large variations in kinetic and thermodynamic properties arise from geometric changes in the ensemble of QM-cluster models, rather from the composition of the QM-cluster models or from the active site-solvent interface. The findings open the way for further quantitative and reproducible calibration in the field of computational enzymology using the model construction framework afforded with the RINRUS software toolkit.
Topics & Concepts
Chorismate mutaseQM/MMMolecular dynamicsCluster (spacecraft)ChemistrySampling (signal processing)WorkflowComputational chemistryStatistical physicsBiological systemPhysicsEnzymeComputer scienceBiologyBiochemistryOpticsDetectorProgramming languageDatabaseBiosynthesisProtein Structure and DynamicsEnzyme Structure and FunctionMetabolomics and Mass Spectrometry Studies