TY - JOUR
AU - Lu, Chin
AB - Background: RNA molecules have been known to play a variety of significant roles in cells. In principle, the functions of RNAs are largely determined by their three-dimensional (3D) structures. As more and more RNA 3D structures are available in the Protein Data Bank (PDB), a bioinformatics tool, which is able to rapidly and accurately search the PDB database for similar RNA 3D structures or substructures, is helpful to understand the structural and functional relationships of RNAs. Results: Since its first release in 2011, R3D-BLAST has become a useful tool for searching the PDB database for similar RNA 3D structures and substructures. It was implemented by a structural-alphabet (SA)-based method, which utilizes an SA with 23 structural letters to encode RNA 3D structures into one-dimensional (1D) structural sequences and applies BLAST to the resulting structural sequences for searching similar substructures of RNAs. In this study, we have upgraded R3D-BLAST to develop a new web server named R3D-BLAST2 based on a higher quality SA newly constructed from a representative and sufficiently non-redundant list of RNA 3D structures. In addition, we have modified the kernel program in R3D-BLAST2 so that it can accept an RNA structure in the mmCIF format as an 
TI - R3D-BLAST2: an improved search tool for similar RNA 3D substructures
JF - BMC Bioinformatics
DO - 10.1186/s12859-017-1956-6
DA - 2017-12-28
UR - https://www.deepdyve.com/lp/springer-journals/r3d-blast2-an-improved-search-tool-for-similar-rna-3d-substructures-KxvL5uNVxg
SP - 31
EP - 38
VL - 18
IS - 16
DP - DeepDyve
ER -