title: R3D-BLAST: a search tool for similar RNA 3D substructures.
abstract: R3D-BLAST is a BLAST-like search tool that allows the user to quickly and accurately search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. The basic idea behind R3D-BLAST is that all the RNA 3D structures deposited in the PDB are first encoded as 1D structural sequences using a structural alphabet of 23 distinct nucleotide conformations, and BLAST is then applied to these 1D structural sequences to search for those RNA substructures whose 1D structural sequences are similar to that of the query RNA substructure. R3D-BLAST takes as input an RNA 3D structure in the PDB format and outputs all substructures of the hits similar to that of the query with a graphical display to show their structural superposition. In addition, each RNA substructure hit found by R3D-BLAST has an associated E-value to measure its statistical significance. R3D-BLAST is now available online at http://genome.cs.nthu.edu.tw/R3D-BLAST/ for public access.
authors.affiliation: Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan.
authors.forename: Yun-Chen
authors.initials: YC
authors.lastname: Liu
authors.forename: Chung-Han
authors.initials: CH
authors.lastname: Yang
authors.forename: Kun-Tze
authors.initials: KT
authors.lastname: Chen
authors.forename: Jyun-Rong
authors.initials: JR
authors.lastname: Wang
authors.forename: Mei-Ling
authors.initials: ML
authors.lastname: Cheng
authors.forename: Jen-Chun
authors.initials: JC
authors.lastname: Chung
authors.forename: Hsien-Tai
authors.initials: HT
authors.lastname: Chiu
authors.forename: Chin Lung
authors.initials: CL
authors.lastname: Lu
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012343:RNA, Transfer / Q000737:chemistry; D012984:Software
chemical_list: D012313:RNA; D012343:RNA, Transfer