title: Automated 3D structure composition for large RNAs.
abstract: Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.
authors.affiliation: Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland.
authors.forename: Mariusz
authors.initials: M
authors.lastname: Popenda
authors.forename: Marta
authors.initials: M
authors.lastname: Szachniuk
authors.forename: Maciej
authors.initials: M
authors.lastname: Antczak
authors.forename: Katarzyna J
authors.initials: KJ
authors.lastname: Purzycka
authors.forename: Piotr
authors.initials: P
authors.lastname: Lukasiak
authors.forename: Natalia
authors.initials: N
authors.lastname: Bartol
authors.forename: Jacek
authors.initials: J
authors.lastname: Blazewicz
authors.forename: Ryszard W
authors.initials: RW
authors.lastname: Adamiak
mesh_terms: D000465:Algorithms; D030561:Databases, Nucleic Acid; D020407:Internet; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012341:RNA, Ribosomal, 5S / Q000737:chemistry; D018626:Retroelements; D012984:Software
chemical_list: D012341:RNA, Ribosomal, 5S; D018626:Retroelements; D012313:RNA