1 - 31 of 31 results

RNAcop / RNA Context Optimization by Probability

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 structure constraints as input. Flanking region lengths are then optimized using energy-based folding into the constrained structure. For example, structure constraints can be derived from comparative RNA structure predictions, prior knowledge from experiments, single sequence folding and pattern search approaches. A strength of RNAcop is to transfer base pairs predicted from multiple related sequence to single sequence folding.

UNAFold / Unified Nucleic Acid Folding

Allows users to simulate nucleic acid folding and hybridization for single-stranded sequences. UNAFold is a program that aims to determine folding for single-stranded RNA or DNA through combination of stochastic sampling, partition function calculations and free energy minimization. To realize melting simulations, it calculates the integrality of melting profile and not only temperatures. Images concerning hybridizations or secondary structure can be compute thanks to common formats.


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, tRNAs, hairpins and ribozymes-and for protein molecules with known 3D structures, as long as they are smaller than 200 amino acid residues. Researchers can determine and understand which elements of the structure limit the folding process for various types of RNAs and protein molecules.


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Allows users to analyze RNA folding spaces. RNAHeliCes is a free software that uses a position-specific abstraction based on helices for extracting structural detail and mapping the structures. The program is based on hishapes computation. For each candidate, the application calculates the hishape, the free energy, the dot-bracket-representation and the partition function contribution of this hishape.


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) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization.


Provides library for RNA energy landscapes. RNAlila offers library functions for investigative exploration of RNA landscape features such as the neighborhood of secondary structures or different types of walks, including adaptive, random and gradient walks starting from a specific structure. It includes two modules: (i) RNAwalk that performs adaptive, gradient or random walks starting from a secondary structure, and (ii) RNArandstruc that computes randomly distributed structures over the Boltzmann ensemble for a RNA sequence.