R3D-BLAST2

RNA molecules play significant roles in cells, and their functions are primarily determined by their three-dimensional (3D) structures. As the number of RNA 3D structures available in the Protein Data Bank (PDB) grows, it becomes increasingly important to have bioinformatics tools that can quickly and accurately search the PDB database for similar RNA 3D structures or substructures. The R3D-BLAST2 web server is an upgraded version of R3D-BLAST, a bioinformatics tool that was first released in 2011 and has since become a valuable resource for searching the PDB for RNA 3D structures and substructures.

R3D-BLAST2 utilizes a structural-alphabet (SA)-based method that encodes RNA 3D structures into one-dimensional (1D) structural sequences using an SA with 23 structural letters. It then applies BLAST to the resulting structural sequences to search for similar substructures of RNAs. This method, combined with the use of a higher quality SA newly constructed from a representative and sufficiently non-redundant list of RNA 3D structures, has resulted in a more accurate and efficient tool for searching the PDB for similar RNA 3D substructures.

One of the key improvements in R3D-BLAST2 is its ability to accept RNA structures in the mmCIF format as input. In addition, experiments on a benchmark dataset have demonstrated that R3D-BLAST2 performs significantly better than its earlier version, R3D-BLAST, and other similar tools, such as RNA FRABASE, FASTR3D, and RAG-3D.