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Nucleic Acids Research Advance Access originally published online on May 12, 2009
Nucleic Acids Research 2009 37(Web Server issue):W287-W295; doi:10.1093/nar/gkp330
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W287-W295
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

FASTR3D: a fast and accurate search tool for similar RNA 3D structures

Chin-En Lai1, Ming-Yuan Tsai1, Yun-Chen Liu1, Chih-Wei Wang1, Kun-Tze Chen1 and Chin Lung Lu1,2,*

1Institute of Bioinformatics and Systems Biology and 2Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan

*To whom correspondence should be addressed. Tel: +886-3-5712121 (ext. 56949); Fax: +886-3-5729288; Email: cllu{at}mail.nctu.edu.tw

Received February 21, 2009. Revised April 15, 2009. Accepted April 19, 2009.

FASTR3D is a web-based search tool that allows the user to fast and accurately search the PDB database for structurally similar RNAs. Currently, it allows the user to input three types of queries: (i) a PDB code of an RNA tertiary structure (default), optionally with specified residue range, (ii) an RNA secondary structure, optionally with primary sequence, in the dot-bracket notation and (iii) an RNA primary sequence in the FASTA format. In addition, the user can run FASTR3D with specifying additional filtering options: (i) the released date of RNA structures in the PDB database, and (ii) the experimental methods used to determine RNA structures and their least resolutions. In the output page, FASTR3D will show the user-queried RNA molecule, as well as user-specified options, followed by a detailed list of identified structurally similar RNAs. Particularly, when queried with RNA tertiary structures, FASTR3D provides a graphical display to show the structural superposition of the query structure and each of identified structures. FASTR3D is now available online at http://bioalgorithm.life.nctu.edu.tw/FASTR3D/.


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