COMPUTER SIMULATION OF PROTEIN DNA COMPLEX

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To study the molecular recognition mechanism between protein and DNA, we have performed molecular dynamics simulations of Zif268-DNA complex. The equilibrium structural properties from simulations are compared with the x-ray crystal structure to evaluate the simulation quality. Simulations are also used to assist the interpretation of experimental data, and short-time scale conformational fluctuation and microscopic structural details which are currently inaccessible to experiments on protein-DNA complex.