Computational investigation of RNA CUG repeats responsible for myotonic dystrophy 1.

ABSTRACT: Despite the importance of the knowledge of molecular hydration entropy (ΔShyd) in chemical and biological processes, the exact calculation of ΔShyd is very difficult, because of the complexity in solute–water interactions. Although free-energy perturbation (FEP) methods have been employed quite widely in the literature, the poor convergent behavior of the van der Waals interaction term in the potential function limited the accuracy and robustness. In this study, we propose a new method for estimating ΔShyd by means of combining the FEP approach and the scaled particle theory (or information theory) to separately calculate the electrostatic solute–water interaction term (ΔSelec) and the hydrophobic contribution approximated by the cavity formation entropy (ΔScav), respectively. Decompositio

SUBMITTER: Yildirim I 

PROVIDER: S-EPMC4606397 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature