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The ViennaRNA Package is software, a set of standalone programs and libraries used for predicting and analysing RNA nucleic acid secondary structures. [1] The source code for the package is released as free and open-source software and compiled binaries are available for the operating systems Linux, macOS, and Windows.
Double-stranded RNA forms an A-type helical structure, unlike the common B-type conformation taken by double-stranded DNA molecules. The secondary structure of RNA consists of a single polynucleotide. Base pairing in RNA occurs when RNA folds between complementarity regions. Both single- and double-stranded regions are often found in RNA molecules.
Sfold is a software program developed to predict probable RNA secondary structures through structure ensemble sampling and centroid predictions [1] [2] with a focus on assessment of RNA target accessibility, [3] for major applications to the rational design of siRNAs [4] in the suppression of gene expressions, and to the identification of targets for regulatory RNAs particularly microRNAs.
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that that the automated ...
CryoEM of nucleic acid has been done on ribosomes, [7] viral RNA, [8] and single-stranded RNA structures within viruses. [ 9 ] [ 10 ] These studies have resolved structural features at different resolutions from the nucleobase level (2-3 angstroms) up to tertiary structure motifs (greater than a nanometer).
List of protein structure prediction software; List of sequence alignment software; List of gene prediction software; List of RNA structure prediction software; Comparison of software for molecular mechanics modeling; List of software for Monte Carlo molecular modeling; List of software for nanostructures modeling; Force field
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