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To bridge the gap between the sequences and 3-dimensional (3D) structures ofRNAs, some computational models have been proposed for predicting RNA 3Dstructures. However, the existed models seldom consider the conditionsdeparting from the room/body temperature and high salt (1M NaCl), and thusgenerally hardly predict the thermodynamics and salt effect. In this study, wepropose a coarse-grained model with implicit salt for RNAs to predict 3Dstructures, stability and salt effect. Combined with Monte Carlo simulatedannealing algorithm and a coarse-grained force field, the model folds 46 testedRNAs (less than or equal to 45 nt) including pseudoknots into their native-likestructures from their sequences, with an overall mean RMSD of 3.5 {\AA} and anoverall minimum RMSD of 1.9 {\AA} from the experimental structures. For 30 RNAhairpins, the present model also gives the reliable predictions for thestability and salt effect with the mean deviation ~ 1.0 degrees Celsius ofmelting temperatures, as compared with the extensive experimental data. Inaddition, the model could provide the ensemble of possible 3D structures for ashort RNA at a given temperature/salt condition.

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