title: Rsite: a computational method to identify the functional sites of noncoding RNAs.
abstract: There is an increasing demand for identifying the functional sites of noncoding RNAs (ncRNAs). Here we introduce a tertiary-structure based computational approach, Rsite, which first calculates the Euclidean distances between each nucleotide and all the other nucleotides in a RNA molecule and then determines the nucleotides that are the extreme points in the distance curve as the functional sites. By analyzing two ncRNAs, tRNA (Lys) and Diels-Alder ribozyme, we demonstrated the efficiency of Rsite. As a result, Rsite recognized all of the known functional sites of the two ncRNAs, suggesting that Rsite could be a potentially useful tool for discovering the functional sites of ncRNAs. The source codes and data sets of Rsite are available at http://www.cuilab.cn/rsite.
authors.affiliation: Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, 38 xueyuan Rd, Beijing. 100191, China.
authors.forename: Pan
authors.initials: P
authors.lastname: Zeng
authors.affiliation: Lab of Translational Biomedicine Informatics, School of Computer Science and Engineering, Hebei University of Technology, 5340 Xiping Rd, Tianjin. 300401, China.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, 38 xueyuan Rd, Beijing. 100191, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Ma
authors.affiliation: Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, 38 xueyuan Rd, Beijing. 100191, China.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Cui
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D016337:RNA, Catalytic / Q000737:chemistry / Q000235:genetics; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics; D022661:RNA, Untranslated / Q000737:chemistry* / Q000235:genetics*; D013329:Structure-Activity Relationship
chemical_list: C518747:Diels-Alder ribozyme; D016337:RNA, Catalytic; D022661:RNA, Untranslated; D012343:RNA, Transfer