COMP 210 |
| The ability to predict conformational equilibria of biomolecules is vital to understanding many important biological processes. The aim of this study is to examine the robustness of the end-point free energy method termed the molecular mechanics Poisson-Boltzmann solvent accessible surface area (MM/PBSA) method. Specifically, applications of MM/PBSA to nucleic acid (NA) systems are explored. MM/PBSA calculations of the free energy difference between A-form and B-form DNA are shown to be in very close agreement with the PMF result determined using an umbrella sampling approach. Further, it is found that the MM/PBSA conformational free energy differences were sensitive to a change from the CHARMM to AMBER force field, however the influence of ionic strength on conformational stability was reproduced very accurately. Finally, a comparison of free energy differences obtained using explicit and implicit solvent models during conformational sampling demonstrates significant differences. |
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Poster Session
6:00 PM-8:00 PM, Tuesday, August 18, 2009 Walter E. Washington Convention Center -- Ballroom A, Poster
Division of Computers in Chemistry |