Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein – ligand interactions
Bhattacharyya M, Vishveshwara S. Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein – ligand interactions. Molecular Omics 2011, 7: 2320-2330. PMID: 21617814, DOI: 10.1039/c1mb05038a.Peer-Reviewed Original ResearchConceptsConformational ensemblesPyrrolysyl-tRNA synthetaseProtein conformational ensemblesImportant biological phenomenaRNA/DNA complexesProtein-ligand interactionsProtein foldingLigand induced variationsConformational populationsDifferent ligandsMD simulation trajectoriesDNA complexesAmino acidsBiological phenomenaSuch subtle changesD. hafnienseSimulation trajectoriesEnzyme catalysisBackbone levelProteinAtomistic detailsNetwork analysisMD snapshotsMolecular dynamics simulationsObjective clustering