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Folding modeling software tools | RNA structure data analysis

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding…
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SimRNA/SimRNAwe…
Web
Desktop

SimRNA/SimRNAweb

Simulates RNA folding and predicts 3D structure. SimRNA is based on a…

Simulates RNA folding and predicts 3D structure. SimRNA is based on a coarse-grained representation of RNA molecules and uses the Monte Carlo method. It can predict RNA 3D structure from sequence…

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Sfold
Web

Sfold

Software for statistical folding of nucleic acids and studies of regulatory…

Software for statistical folding of nucleic acids and studies of regulatory RNAs.

Kinefold
Web

Kinefold

Provides a web interface for stochastic folding simulations of nucleic acids on…

Provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales.

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pKiss
Desktop
Web

pKiss

A tool for folding RNA secondary structures, including two limited classes of…

A tool for folding RNA secondary structures, including two limited classes of pseudoknots. As pKiss is the successor of pknotsRG, the first pseudoknot class is the canonical simple recursive…

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MONSTER
Desktop

MONSTER

Enables users to detect structural motifs shared between two RNAs. MONSTER is…

Enables users to detect structural motifs shared between two RNAs. MONSTER is composed of two main core modules (i) to assign a unique structure to the reference RNA encoded by a set of Non Branching…

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Context Fold
Web
Desktop

Context Fold

Increase the amount of information used by RNA folding prediction models to the…

Increase the amount of information used by RNA folding prediction models to the improvement of their prediction quality. It is shown that the application of more precise models with Context Fold…

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RNAcop
Desktop
Web

RNAcop RNA Context Optimization by Probability

A computational framework for evaluating the influence of different lengths of…

A computational framework for evaluating the influence of different lengths of flanking regions on folding a single sequence into a specified structure. RNAcop takes the single sequence and the…

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MXfold
Desktop

MXfold MaX-margin based rna FOLDing algorithm

Provides a method for RNA secondary structure prediction. MXfold combines a…

Provides a method for RNA secondary structure prediction. MXfold combines a machine learning based weighted and a thermodynamic approach to perform an accurate prediction in unobserved substructures.…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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HiRE-RNA
Desktop

HiRE-RNA

Allows to manipulate RNA structures interactively. HiRE-RNA is a coarse-grained…

Allows to manipulate RNA structures interactively. HiRE-RNA is a coarse-grained model for RNA structure prediction and the dynamical study of RNA folding. By mean of a molecular visualization…

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FoldNucleus
Web

FoldNucleus

Predicts RNA and protein folding nuclei from their 3D structures. Using…

Predicts RNA and protein folding nuclei from their 3D structures. Using FoldNucleus, it is possible to calculate the folding nucleus for RNA molecules with known 3D structures-including pseudoknots,…

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KnotInFrame
Desktop
Web

KnotInFrame

An algorithm for the automatic detection of -1 PRF signals from genomic…

An algorithm for the automatic detection of -1 PRF signals from genomic sequences. KnotInFrame finds the frameshifting stimulators by means of a specialized RNA-pseudoknot folding program, fast…

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TBI
Web

TBI Tightly Bound Ion

A tool for predicting ion effects in RNA folding. TBI predicts the…

A tool for predicting ion effects in RNA folding. TBI predicts the electrostatic free energy, the different free energy components, the average binding fraction of ions, and the most probable ion…

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SparseMFEFold
Desktop

SparseMFEFold

An elegant and practical solution which introduces garbage collection as a…

An elegant and practical solution which introduces garbage collection as a novel technique to RNA folding. SparseMFEFold outperforms RNAfold both in terms of time and space. We note that this…

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Vfold
Web
Desktop

Vfold

Provides a user friendly tool for the prediction of RNA structure and…

Provides a user friendly tool for the prediction of RNA structure and stability. Vfold offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b)…

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barriers
Desktop

barriers

Computes barriers trees of a landscape. barriers provides a software able to…

Computes barriers trees of a landscape. barriers provides a software able to calculate the saddle points in an arbitrary landscape and builds a barrier tree from an energy or cost sorted list of…

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segmentation-fo…
Desktop

segmentation-fold

Predicts RNA 2D-structure with an extended version of the Zuker algorithm.…

Predicts RNA 2D-structure with an extended version of the Zuker algorithm. segmentation-fold is a bioinformatics application implemented in C++ that contains two structure elements: the segment and…

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UNAFold
Web

UNAFold Unified Nucleic Acid Folding

An integrated collection of programs that simulate folding, hybridization, and…

An integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. Folding (secondary structure) prediction for…

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COFOLD
Desktop
Web

COFOLD

A method for predicting RNA secondary structure that takes effects of…

A method for predicting RNA secondary structure that takes effects of co-transcriptional folding explicitly into account. COFOLD significantly improves the state-of-art in terms of prediction…

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