A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.

ABSTRACT: The computational efficiency of approximate quantum mechanical methods allows their use for the construction of multidimensional reaction free energy profiles. It has recently been demonstrated that quantum models based on the neglect of diatomic differential overlap (NNDO) approximation have difficulty modeling deoxyribose and ribose sugar ring puckers and thus limit their predictive value in the study of RNA and DNA systems. A method has been introduced in our previous work to improve the description of the sugar puckering conformational landscape that uses a multidimensional B-spline correction map (BMAP correction) for systems involving intrinsically coupled torsion angles. This method greatly improved the adiabatic potential energy surface profiles of DNA and RNA sugar rings relative

SUBMITTER: Huang M 

PROVIDER: S-EPMC5839098 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature