ARTS: alignment of RNA tertiary structures.

@article{citeulike:361886, abstract = {MOTIVATION: A fast growing number of non-coding RNAs have recently been discovered to play essential roles in many cellular processes. Similar to proteins, understanding the functions of these active RNAs requires methods for analyzing their tertiary structures. However, in contrast to the wide range of structure-based approaches available for proteins, there is still a lack of methods for studying RNA structures. RESULTS: We present a new computational method named ARTS (alignment of RNA tertiary structures). The method compares two nucleic acid structures (RNAs or DNAs) and detects a-priori unknown common substructures. These substructures can be either large global folds containing hundreds and even thousands of nucleotides or small local tertiary motifs with at least two successive base pairs. To the best of our knowledge, this is the first method of this type. The method is highly-efficient and was used to conduct an all-against-all comparison of all the RNA structures currently available in the Protein Data Bank. AVAILABILITY: The program, a web-server and supplementary information are available on http://bioinfo3d.cs.tau.ac.il/ARTS CONTACT: oranit@post.tau.ac.il.}, address = {School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University Tel Aviv 69978, Israel.}, author = {Dror, O. and Nussinov, R. and Wolfson, H. }, citeulike-article-id = {361886}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {algorithms, rna, structure\_alignment}, month = {September}, posted-at = {2005-10-23 03:11:36}, priority = {4}, title = {ARTS: alignment of RNA tertiary structures.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/16204124}, volume = {21 Suppl 2}, year = {2005} }

TY - JOUR ID - citeulike:361886 L3 - citeulike-article-id:361886 TI - ARTS: alignment of RNA tertiary structures. JF - Bioinformatics VL - 21 Suppl 2 AD - School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University Tel Aviv 69978, Israel. SN - 1367-4803 N2 - MOTIVATION: A fast growing number of non-coding RNAs have recently been discovered to play essential roles in many cellular processes. Similar to proteins, understanding the functions of these active RNAs requires methods for analyzing their tertiary structures. However, in contrast to the wide range of structure-based approaches available for proteins, there is still a lack of methods for studying RNA structures. RESULTS: We present a new computational method named ARTS (alignment of RNA tertiary structures). The method compares two nucleic acid structures (RNAs or DNAs) and detects a-priori unknown common substructures. These substructures can be either large global folds containing hundreds and even thousands of nucleotides or small local tertiary motifs with at least two successive base pairs. To the best of our knowledge, this is the first method of this type. The method is highly-efficient and was used to conduct an all-against-all comparison of all the RNA structures currently available in the Protein Data Bank. AVAILABILITY: The program, a web-server and supplementary information are available on http://bioinfo3d.cs.tau.ac.il/ARTS CONTACT: oranit@post.tau.ac.il. KW - algorithms KW - rna KW - structure_alignment AU - Dror, O AU - Nussinov, R AU - Wolfson, H PY - 2005/09/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/16204124 ER -