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Tertiary structure prediction software tools | RNA data analysis

A deeper knowledge of complex RNA structures is essential to understand their new biological functions.

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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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DSSR
Desktop

DSSR Dissecting the Spatial Structure of RNA

An integrated and automated tool for analyzing and annotating RNA tertiary…

An integrated and automated tool for analyzing and annotating RNA tertiary structures. DSSR identifies canonical and noncanonical base pairs, including those with modified nucleotides, in any…

MINT
Desktop
Web

MINT Motif Identifier for Nucleic acids Trajectory

An automatic tool for analyzing three-dimensional structures of RNA and DNA,…

An automatic tool for analyzing three-dimensional structures of RNA and DNA, and their full-atom molecular dynamics trajectories or other conformation sets (e.g. X-ray or nuclear magnetic…

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RNAshapes
Desktop
Web

RNAshapes

A software package that integrates three RNA analysis tools based on the…

A software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus…

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baRNAba
Desktop

baRNAba

A minimalist representation of RNA three-dimensional structures that solely…

A minimalist representation of RNA three-dimensional structures that solely considers the relative orientation and position of nucleobases. Based on this representation, baRNAba is a tool for…

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RNA-MoIP
Web

RNA-MoIP RNA Motifs over Integer Programming

Uses an integer programming framework to predict RNA 2D-3D structures. RNA-MoIP…

Uses an integer programming framework to predict RNA 2D-3D structures. RNA-MoIP is an accurate hybrid method that uses RNA secondary structure templates in which it inserts candidate RNA 3D motifs.…

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RNA 3D Motif…
Dataset

RNA 3D Motif Atlas

Offers an automated pipeline based on a comprehensive framework for extracting,…

Offers an automated pipeline based on a comprehensive framework for extracting, analyzing, and classifying RNA 3D motifs. RNA 3D motif atlas is a comprehensive and representative collection of…

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RNA Base…
Dataset

RNA Base Triples Database

Hosts observed and modeled base triples, organized in two ways, by geometric…

Hosts observed and modeled base triples, organized in two ways, by geometric triple family and by three-base combination. The RNA Base Triples Database provides separate web pages for each base…

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NAFlex
Web

NAFlex Nucleic Acids Flexibility

A web tool to study the flexibility of nucleic acids, either isolated or bound…

A web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. NAFlex integrates a variety of analysis packages for mining nucleic acid trajectories. Analysis…

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R3D-2-MSA
Web

R3D-2-MSA RNA 3D Structure-to-Multiple Sequence Alignment

Provides seamless, nucleotide-level access to high-quality, curated sequence…

Provides seamless, nucleotide-level access to high-quality, curated sequence alignments for rRNAs of all major phylogenetic domains, using residue numbers taken directly from representative,…

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3dRNAscore
Desktop

3dRNAscore

A knowledge-based potential that combines distance-dependent and…

A knowledge-based potential that combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing…

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GARN
Desktop

GARN Game Algorithm for RNa sampling

A software to compute a sampling of RNA 3D structure from a secondary…

A software to compute a sampling of RNA 3D structure from a secondary structure. GARN is a coarse-grained method for sampling, based on game theory and knowledge-based potentials. Game theory is a…

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iFoldRNA
Desktop
Web

iFoldRNA

Allows accurate prediction of short (<50 nucleotides) tertiary RNA…

Allows accurate prediction of short (<50 nucleotides) tertiary RNA structures starting from primary sequences. The new version of the iFoldRNA server permits the prediction of tertiary structure…

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CRWrnafold
Web

CRWrnafold

A new version of RNAfold that uses statistical potentials derived from…

A new version of RNAfold that uses statistical potentials derived from comparative data.

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Ring Catalog
Dataset

Ring Catalog

An in silico solution to this design problem by combinatorial assembly of RNA…

An in silico solution to this design problem by combinatorial assembly of RNA 3-way junctions, bulges, and kissing loops, and tabulating the cases that lead to ring formation. The identified ring…

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COGNAC
Web

COGNAC COnnection tables Graphs for Nucleic ACids

A graph theoretical algorithm implemented as a web server that is able to…

A graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA…

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RNA Bricks
Dataset

RNA Bricks

Stores information about recurrent RNA 3D motifs and their interactions, found…

Stores information about recurrent RNA 3D motifs and their interactions, found in experimentally determined RNA structures and in RNA-protein complexes. Besides, the search utility enables searching…

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ClaRNA
Web

ClaRNA

A method for computational classification of contacts in RNA 3D structures.

A method for computational classification of contacts in RNA 3D structures.

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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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BkTree
Desktop

BkTree

A method to tackle a key step in the RNA 3D structure prediction problem, the…

A method to tackle a key step in the RNA 3D structure prediction problem, the prediction of the nucleotide interactions that constitute the desired 3D structure. The research is based on a novel…

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RNAdualPF
Desktop

RNAdualPF RNAdual Partition Function

Computes the dual partition function Z of all RNA nucleotide sequences a…

Computes the dual partition function Z of all RNA nucleotide sequences a compatible with target structure s0. RNAdualPF generates sequences which have low free energy with respect to a user-specified…

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RSIM
Desktop

RSIM

Proposes an RNA fragment assembly method that preserves RNA global secondary…

Proposes an RNA fragment assembly method that preserves RNA global secondary structure while sampling conformations. RSIM provides a fully automated application predicting RNA tertiary structures…

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Ernwin
Desktop

Ernwin

A program for sampling coarse grain 3D RNA structures. Ernwin uses the coarse…

A program for sampling coarse grain 3D RNA structures. Ernwin uses the coarse grain representation presented in the forgi library. The simplest scenario involves providing a sequence and a secondary…

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RNAexpNumNbors
Desktop
Web

RNAexpNumNbors

An algorithm that can compute the expected number of neighbors, or expected…

An algorithm that can compute the expected number of neighbors, or expected network degree, of an input sequence. For RNA sequences from the Rfam database, the expected degree is significantly less…

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NCIR
Dataset

NCIR

Provides rapid access to all the RNA structures in which a particular, rare…

Provides rapid access to all the RNA structures in which a particular, rare base–base interaction has been observed. NCIR also summarizes the important properties that have been associated with…

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RNAComposer
Web

RNAComposer

Offers a user-friendly approach to the fully automated prediction of large RNA…

Offers a user-friendly approach to the fully automated prediction of large RNA 3D structures.

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RNAlyzer
Desktop

RNAlyzer

A computational method for comparison of RNA 3D models with the reference…

A computational method for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models.

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RNAentropy
Desktop
Web

RNAentropy

Implements two cubic time algorithms to compute the RNA thermodynamic…

Implements two cubic time algorithms to compute the RNA thermodynamic structural entropy H(s) of a sequence s. Structural entropy is computed from the expected free energy of the sequence <E>…

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PTRNAmark
Desktop

PTRNAmark Precision Training RNA Mark

An algorithm to evaluate 3D RNA structure. PTRNAmark doesn’t only combine…

An algorithm to evaluate 3D RNA structure. PTRNAmark doesn’t only combine nucleotides’ mutual and self energies but also fully considers the specificity of every RNA. It is based on…

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NASSAM
Web

NASSAM Nucleic Acids Search for Substructures and Motifs

A graph theoretical program that can search for 3D patterns of base…

A graph theoretical program that can search for 3D patterns of base arrangements by representing the bases as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern…

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TRFolder-W
Desktop
Web

TRFolder-W

A web server capable of predicting core structures of telomerase RNA (TR) in…

A web server capable of predicting core structures of telomerase RNA (TR) in yeast genomes. The aim of TRFolder-W is to use the five core structures as fundamental units to predict potential TR genes…

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WebFR3D
Desktop
Web

WebFR3D

A program for annotating atomic-resolution RNA 3D structure files and searching…

A program for annotating atomic-resolution RNA 3D structure files and searching them efficiently to locate and compare RNA 3D structural motifs. WebFR3D provides on-line access to the central…

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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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WebRASP
Desktop
Web

WebRASP

Computes energy scores for assessing the stability of RNA structures. WebRASP…

Computes energy scores for assessing the stability of RNA structures. WebRASP receives as input a PDB file containing the atomic coordinates of the RNA structure and calculates the energy profile and…

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ModeRNA
Web

ModeRNA

A program for comparative modeling of RNA 3D structures.

A program for comparative modeling of RNA 3D structures.

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NAST
Desktop

NAST Nucleic Acid Simulation Tool

A software tool for RNA modeling that uses an RNA-specific knowledge-based…

A software tool for RNA modeling that uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate plausible 3D structures. We demonstrate NAST's…

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RNA-Puzzles
Dataset

RNA-Puzzles

A collective experiment for blind RNA structure prediction.

A collective experiment for blind RNA structure prediction.

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NanoTiler
Desktop

NanoTiler

A Java application for the design of RNA nanoscale structures from building…

A Java application for the design of RNA nanoscale structures from building blocks. Among other things, it can accomplish the following: 1) detection, extraction and annotation of RNA structural…

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RNA2D3D
Desktop

RNA2D3D

Using primary and secondary structure information of an RNA molecule, the…

Using primary and secondary structure information of an RNA molecule, the program automatically and rapidly produces a first-order approximation of a 3-dimensional conformation consistent with this…

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RNAssess
Web

RNAssess

A computational server for comparison of RNA 3D models with the reference…

A computational server for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models. Our approach is based on the idea of local…

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SCOR
Dataset

SCOR Structural Classification Of RNA

Provides a comprehensive perspective and understanding of RNA motif…

Provides a comprehensive perspective and understanding of RNA motif three-dimensional structure, function, tertiary interactions and their relationships. The web interface provides a straightforward…

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