Browsing by Author "Liu, Yun-Chen"

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FASTR3D: a fast and accurate search tool for similar RNA 3D structures
(2009-07-01)
Lai, Chin-En
;
Tsai, Ming-Yuan
;
Liu, Yun-Chen
;
Wang, Chih-Wei
;
Chen, Kun-Tze
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/.
R3D-BLAST: a search tool for similar RNA 3D substructures
(2011-07-01)
Liu, Yun-Chen
;
Yang, Chung-Han
;
Chen, Kun-Tze
;
Wang, Jyun-Rong
;
Cheng, Mei-Ling
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.