title: A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling.
abstract: Accurate tertiary structures are very important for the functional study of non-coding RNA molecules. However, predicting RNA tertiary structures is extremely challenging, because of a large conformation space to be explored and lack of an accurate scoring function differentiating the native structure from decoys. The fragment-based conformation sampling method (e.g. FARNA) bears shortcomings that the limited size of a fragment library makes it infeasible to represent all possible conformations well. A recent dynamic Bayesian network method, BARNACLE, overcomes the issue of fragment assembly. In addition, neither of these methods makes use of sequence information in sampling conformations. Here, we present a new probabilistic graphical model, conditional random fields (CRFs), to model RNA sequence-structure relationship, which enables us to accurately estimate the probability of an RNA conformation from sequence. Coupled with a novel tree-guided sampling scheme, our CRF model is then applied to RNA conformation sampling. Experimental results show that our CRF method can model RNA sequence-structure relationship well and sequence information is important for conformation sampling. Our method, named as TreeFolder, generates a much higher percentage of native-like decoys than FARNA and BARNACLE, although we use the same simple energy function as BARNACLE.
  
  
  BACKGROUND
  zywang@ttic.edu; j3xu@ttic.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Toyota Technological Institute at Chicago, IL, USA. zywang@ttic.edu
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Wang
authors.forename: Jinbo
authors.initials: J
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D011336:Probability; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D012313:RNA