Classical Molecular Dynamics Simulations of Proteins：经典的蛋白质的分子动力学模拟.pptVIP

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Classical Molecular Dynamics Simulations of Proteins：经典的蛋白质的分子动力学模拟.ppt

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Classical Molecular Dynamics Simulations of Proteins：经典的蛋白质的分子动力学模拟

Protein Folding BiospectroscopyLecture 5 F14PFB David Robinson Protein Folding Introduction Protein Structure Interactions Protein Folding Models Biomolecular Modelling Bioinformatics Classical Molecular Dynamics Simulations of Proteins “everything that living things do can be understood in terms of the jigglings and wigglings of atoms.” The Feynman Lectures in Physics vol. 1, 3-6 (1963) What is Molecular Dynamics? “The science of simulating the motions of a system of particles” (Karplus Petsko) From systems As small as an atom As large as a galaxy Equations of motion Time evolution Why? Essential Elements Knowledge of the interaction potential for the particles Forces Classical Newtonian equations of motion Many particle systems simulation Maxwell-Boltzmann averaging process for thermodynamic properties: time averaging One particle easy analytically Many particles impossible analytically Basis: Molecular Mechanics Theoretical foundation Potential energy functions Energy minimization Molecular dynamics Uses of simulation modelling Conformational searching with MD and minimization Exploration of biopolymer fluctuations and dynamics kinetics MD as an ensemble sampler Free energy simulations Example applications Energy minimization as an estimator of binding free energies Protein stability Approximate association free energy of molecular assemblies Approximate pKa calculations Theoretical Foundations Force field parameters for families of chemical compounds System modelled using Newton’s equations of motion Examples: hard spheres simulations (Alder Wainwright, 1959); Liquid water (Rahman Stillinger, 1970); BPTI (McCammon Karplus, 1976); Villin headpiece (Duan Kollman, 1998) Protein Motion Protein motions of importance are torsional oscillations about the bonds that link groups together Substantial displacements of groups occur over long time intervals Collective motions either local (cage structure) or rigid-body (displacement of different