title: Structure Prediction of RNA Loops with a Probabilistic Approach.
abstract: The knowledge of the tertiary structure of RNA loops is important for understanding their functions. In this work we develop an efficient approach named RNApps, specifically designed for predicting the tertiary structure of RNA loops, including hairpin loops, internal loops, and multi-way junction loops. It includes a probabilistic coarse-grained RNA model, an all-atom statistical energy function, a sequential Monte Carlo growth algorithm, and a simulated annealing procedure. The approach is tested with a dataset including nine RNA loops, a 23S ribosomal RNA, and a large dataset containing 876 RNAs. The performance is evaluated and compared with a homology modeling based predictor and an ab initio predictor. It is found that RNApps has comparable performance with the former one and outdoes the latter in terms of structure predictions. The approach holds great promise for accurate and efficient RNA tertiary structure prediction.
authors: National Laboratory of Solid State Microstructures, School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China.
authors: Jun
authors: J
authors: Li
authors: National Laboratory of Solid State Microstructures, School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China.
authors: Jian
authors: J
authors: Zhang
authors: National Laboratory of Solid State Microstructures, School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China.
authors: Jun
authors: J
authors: Wang
authors: National Laboratory of Solid State Microstructures, School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China.
authors: Wenfei
authors: W
authors: Li
authors: National Laboratory of Solid State Microstructures, School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China.
authors: Wei
authors: W
authors: Wang
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D015233:Models, Statistical; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: D012313:RNA