Computer Simulation and the Design of New Biological Molecules

<div class="line" id="line-13"> <span style='color: rgb(28, 29, 30); font-family: "Open Sans", icomoon, sans-serif; font-size: 16px;'> Molecular dynamics simulations have been carried out for the enzyme bovine trypsin, for the small inhibitor benzamidine, and for the complex formed by these two molecules, all in the presence of enough water to approximate dilute solution conditions. The simulations have been analyzed to characterize the structure and dynamics of the enzyme and its solvent surroundings. Using the recently developed thermodynamic cycle&hyphen;perturbation method, the simulations have also been analyzed to determine how changes in the structure of the enzyme and the inhibitor alter the free energy of complex formation. The results suggest that such simulations may be useful in the design of new enzymes and enzyme inhibitors. </span></div>