?Free energy calculation and sampling conformational ensemble for protein folding and protein-ligand binding?Searching new ligand-binding site from database based on similarity of local 3D structure?Developing coarse-grained model of biomolecule to study effects of post-translational modification (e.g. phosphorylation) on intermolecular interactionBDMoleculeーStructure ー?theoretical models?dynamics, flexibility?solvationMolecular simulationstructure-activity relationship Understandingligand-binding mechanismActivityComputationalーFunction ー?binding partner?active conformation?affinity, kinetics …StructuralBiologyDatabase analysisNew knowledge ofBindingprocessmodification?signaling?32Biotechnology DivisionLaboratory of FunctionalMolecular DesignKojiUMEZAWAAssistantProfessor,Ph.D.Bioinformatics,Biophysics, Molecular Dynamics Simulation, Molecular Modeling, Computational Structural BiologyMoleculehasalotofpossibleconformationsatroomtemperature.Thereshouldbeabiologicallyactiveconformation.Theactiveconformationisinterestingandprovidesakeytointerpretthebiologicalfunction.However,itisdifficulttocharacterizethatconformation.Then,wehaveusedmoleculardynamicssimulationanddatabaseanalysistofigureouttherelationshipofmolecularconformationanddynamicswiththebiologicalactivitysuchasproteinfolding,ligandrecognition,post-translationalmodificationeffects,andligand-association/dissociationcontrol.Ourcurrenttopicsdescribedbelowhavebeenstudied.Relationship between structural information and Cfunction has been explored computationally.In silico study?Molecular modeling?ProgramingWe have developed molecular modeling and programing to study ligand-binding mechanism.
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