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Protocols

ProbKnot specifications

Information


Unique identifier OMICS_03462
Name ProbKnot
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for ProbKnot

ProbKnot citations

 (7)
library_books

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs

2017
Nucleic Acids Res
PMCID: 5714223
PMID: 29036420
DOI: 10.1093/nar/gkx815

[…] to compose a structure with base pairs with estimated base pairing probabilities higher than threshold, using the maximum expected accuracy (MEA) secondary structure prediction algorithm (–), or the ProbKnot method (,). TurboFold is iterative, with the extrinsic information being updated with each iteration, and the iterations were shown to improve the accuracy of the base pairing probability est […]

call_split

A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction

2017
Nucleic Acids Res
PMCID: 5449625
PMID: 28334976
DOI: 10.1093/nar/gkx170
call_split See protocol

[…] Calculations were performed using the RNAstructure package (). Specifically, partition function (program partition) (), stochastic sampling (program stochastic), ProbKnot (), secondary structure comparison (program scorer) and the folding free energy calculator (program efn2) were used. […]

library_books

Nuclear Magnetic Resonance Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction Dependent Chemical Shift Constraints

2015
Biochemistry
PMCID: 4666457
PMID: 26451676
DOI: 10.1021/acs.biochem.5b00833

[…] esis (H0), stating that NAPSS-CS is not more accurate than an alternative program, was tested. Constrained NAPSS-CS was found to have a sensitivity (p < 0.05) significantly higher than those of Fold, ProbKnot, and ShapeKnots, and a PPV significantly higher than that of ProbKnot ().For structures with pseudoknots, the sensitivity and PPV for pseudoknotted base pairs were calculated separately with […]

library_books

Characteristics and Prediction of RNA Structure

2014
Biomed Res Int
PMCID: 4109605
PMID: 25110687
DOI: 10.1155/2014/690340

[…] ich includes 47 sequences from PseudoBase and PDB, which is also a subset of those used in the HotKnots.We present the prediction results of our method compared with those of HotKnots [], McQfold [], ProbKnot [], TT2NE [], Mfold [], and LZ []. MFold is restricted to secondary structures that are free of pseudoknots, whereas others can result in any topology of pseudoknot.This set includes most of […]

library_books

Accelerating calculations of RNA secondary structure partition functions using GPUs

2013
PMCID: 4175106
PMID: 24180434
DOI: 10.1186/1748-7188-8-29

[…] prediction for sequences of this size and most likely substantially larger.We also used the calculated base pair probabilities to determine a single consensus structure for each sequences, using the ProbKnot algorithm []. In this case, working in single precision led to differences with double precision only for one sequence (a random sequence of 6000 bases) out of the 44 we examined, and these w […]

library_books

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

2013
Nucleic Acids Res
PMCID: 3627593
PMID: 23435231
DOI: 10.1093/nar/gkt101

[…] all predictions for those sequences in the RNAstrand data set, for which CompaRNA managed to assign an Rfam family—apart from ContextFold and UNAFold, these were IPknot, Contrafold, Sfold, MaxExpect, ProbKnot, Fold and RNAfold. The most robust comparative method turned out to be MXScarna—when run with a query comprising all sequences from the Rfam seed alignment, it generated predictions for 36.6% […]

Citations

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ProbKnot institution(s)
Department of Biochemistry and Biophysics, University of Rochester Medical Center, Chinahester, NY, USA; Center for RNA Biology, University of Rochester Medical Center, Chinahester, NY, USA; Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Chinahester, NY, USA

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