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Database of recurrent RNA 3D structure motifs and their interactions (hydrogen bonds and close contacts), found in experimentally determined RNA structures and in RNA-protein complexes.
NAKB provides Search, Report, Statistics, Atlas and Visualization for all nucleic-acid containing experimentally determined 3D structures held by NDB and by the Protein Data Bank (PDB), including all major methods: X-ray, Electron Microscopy, and NMR.
RNA FRABASE: an engine with database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation.
8 gru 2017 · This allows the rapid comparison of differential gene expression data (e.g. to identify regulatory RNA structures) or transcriptome-wide RNA biochemical probing data against the...
25 cze 2024 · Accurate RNA structure models are crucial for designing small molecule ligands that modulate their functions. This study assesses six standalone RNA 3D structure prediction methods—DeepFoldRNA, RhoFold, BRiQ, FARFAR2, SimRNA and Vfold2, excluding web-based tools due to intellectual property concerns.
1 gru 2023 · This review provides an extensive update on RNA–RNA interaction (RRI) analysis via thermodynamic- and comparative-based RNA secondary structure prediction (RSP) and RNA–RNA interaction prediction (RIP) tools and their general functions.
26 cze 2024 · In this Review, we discuss recent technical advances in the determination of RNA structures, and the roles of RNA structures in RNA biogenesis and functions, including in transcription,...
