Utility of potential energy span as an approximate free energy proxy
Abstract
Free energy calculation is critical in predictive tasks such as protein folding, docking and design. However, rigorous calculation of free energy change is prohibitively expensive in these practical applications. The minimum potential energy is therefore widely utilized to approximate free energy. In this study, based on analysis of extensive molecular dynamics (MD) simulation trajectories of a few native globular proteins, we found that change of minimum and corresponding maximum potential energy terms exhibit similar level of correlation with change of free energy. More importantly, we demonstrated that change of span (maximum  minimum) of potential energy terms, which engender negligible additional computational cost, exhibit considerably stronger correlations with change of free energy than the corresponding change of minimum and maximum potential energy terms. Therefore, potential energy span may serve as an alternative efficient approximate free energy proxy.
 Publication:

arXiv eprints
 Pub Date:
 March 2016
 arXiv:
 arXiv:1603.01794
 Bibcode:
 2016arXiv160301794W
 Keywords:

 Quantitative Biology  Biomolecules
 EPrint:
 18 pages, 8 figures