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Protocols

RNAKinetics specifications

Information


Unique identifier OMICS_30971
Name RNAKinetics
Interface Web user interface
Restrictions to use None
Input data A RNA sequence, a chain elongation constant, a nucleation constant, the final time of the simulation, and the number of runs of the simulation.
Input format FASTA
Programming languages Java
Computer skills Basic
Stability No
Maintained No

Publication for RNAKinetics

RNAKinetics citations

 (5)
library_books

Computational Methods for Modeling Aptamers and Designing Riboswitches

2017
Int J Mol Sci
PMCID: 5713409
PMID: 29149090
DOI: 10.3390/ijms18112442

[…] ances the conformation sampling, can be used to study the large scale conformational fluctuations of RNAs.Also based on the coarse-grained structural model, a number of computational methods, such as RNAkinetics [], Kinefold [], and COFOLD [] are developed to simulate co-transcriptional folding pathways of mRNAs from the early 1980s when key experiments show that structure formation happens co-tra […]

library_books

Network Properties of the Ensemble of RNA Structures

2015
PLoS One
PMCID: 4619022
PMID: 26488894
DOI: 10.1371/journal.pone.0139476

[…] of RNA folding rates, and due in part to the notorious difficulty of estimating RNA secondary structure folding rates when using secondary structure kinetics software such as Kinfold [], Kinefold [], RNAKinetics [], KFold [], or other software [, ]. Such programs implement an event-driven Monte Carlo algorithm known as Gillespie’s algorithm []; it follows that repeated (time-consuming) simulations […]

call_split

Transient RNA structure features are evolutionarily conserved and can be computationally predicted

2013
Nucleic Acids Res
PMCID: 3695514
PMID: 23625966
DOI: 10.1093/nar/gkt319
call_split See protocol

[…] vised an analysis pipeline that performs folding simulations on several homologous sequences that derive from the same data set. We have chosen three simulation methods: Kinéfold (), Kinwalker () and RNAKinetics (). These represent the diversity of existing folding simulation methods, differ significantly in their simulation algorithms and are freely available.Kinéfold and RNAKinetics both use sto […]

library_books

Efficient procedures for the numerical simulation of mid size RNA kinetics

2012
PMCID: 3463434
PMID: 22958879
DOI: 10.1186/1748-7188-7-24

[…] review of the field is available in []. Other computational simulation approaches for RNA kinetics besides Kinfold [] that are beyond the regime of the mid-size RNA kinetics described herein include RNAkinetics [], Kinefold [], and Kinwalker [] for large RNAs. To further motivate the time-dependent view, it was shown in [] that RNA genes not only encode information about their functional structur […]

library_books

Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo Knotted and Alternative Structures

2010
PLoS Comput Biol
PMCID: 2891591
PMID: 20589081
DOI: 10.1371/journal.pcbi.1000823

[…] generally not feasible to calculate the full transition matrix. However, folding trajectories can be sampled using Monte Carlo stochastic simulation of the Markov process. Several programs, including RNAkinetics –, Kinfold and Kinefold –, employ this method, though they differ significantly in their implementation.Mironov and Lebedev were the first to model the co-transcriptional folding of an e […]

Citations

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RNAKinetics institution(s)
Institute for Problems of Information Transition RAS, Moscow, Russia; Departement of Bioengineering and Bioinformatics, Moscow State University, Laboratory Bldg B, Moscow, Russia; Center for BioDynamics, Boston University, Boston, MA, USA; State Scientific Centre “GosNIIGenetika”, Moscow, Russia
RNAKinetics funding source(s)
Supported in part by grants from Howard Hughes Medical Institute (55000309), Ludwig Institute for Cancer Research (CRDF RBO-1268) and RFBR (04-04-49438).

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