Before revision:  MD simulations coupled with MMPBSA binding free energy calculations were used to analyze scenarios described in prior studies concerning the nature of anti-ABeta antibody binding to various ABeta species. Finally, based on observing our MD trajectories of the PFA1 antibody bound to ABeta_2-7 and pE3ABeta_3-8 ,  we introduced rational mutations into PFA1 in an effort to improve the calculated binding affinity of PFA1 towards the pE3-ABeta_3-8 form of ABeta.
After revision:  MD simulations coupled with MMPBSA binding free energy calculations were used to analyze scenarios described in prior studies , we introduced rational mutations into PFA1 in an effort to improve the calculated binding affinity of PFA1 towards the pE3-ABeta_3-8 form of ABeta.