Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing.

A physics-based method for the prediction of the structures of nucleic acids, which is based on the physics-based 2-bead NARES-2P model of polynucleotides and global-optimization Conformational Space Annealing (CSA) algorithm has been proposed. The target structure is sought as the global-energy-minimum structure, which ignores the entropy component of the free energy but spares expensive multicanonical simulations necessary to find the conformational ensemble with the lowest free energy. The CSA algorithm has been modified to optimize its performance when treating both single and multi-chain nucleic acids. It was shown that the method finds the native fold for simple RNA molecules and DNA duplexes and with limited distance restraints, which can easily be obtained from the secondary-structure-prediction servers, complex RNA folds can be treated with using moderate computer resources.