A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect

To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grained model with implicit salt for RNAs to predict 3D structures, stability, and salt effect. Combined with Monte Carlo simulated annealing algorithm and a coarse-grained force field, the model folds 46 tested RNAs (<= 45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 angstrom and an overall minimum RMSD 1.9 angstrom from the experiment structures. For 30 RNA hairpins, the present model also gives the reliable predictions for the stability and salt effect with the mean deviation similar to 1.0 degrees C of melting temperatures, as compared with the extensive experimental data. In addition, the model could provide the ensemble of possible 3D structures for a short RNA at a given temperature/salt condition. (C) 2014 AIP Publishing LLC.