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 in publications

 (4)
PMCID: 5449625
PMID: 28334976
DOI: 10.1093/nar/gkx170

[…] have been reported previously., 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., this work used the 2004 set of folding free energy parameters. […]

PMCID: 4109605
PMID: 25110687
DOI: 10.1155/2014/690340

[…] folding rna structures according to the above golden section points. the sensitivity and number of predicted pseudoknots of our algorithm are better than those of the mfold, hotknots, mcqfold, probknot, and lhw-zhu algorithms. experimental results reflect the folding rules of rna from a new angle that is close to natural folding., rnas are versatile molecules. messenger rnas carry genetic […]

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

[…] 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, […]

PMCID: 3406180
PMID: 22911650
DOI: 10.1371/journal.pgen.1002840

[…] to rna secondary structure analysis via rnastructure version 5.3 . folding was performed using the partition function algorithm, which enables the prediction of putative rna pseudoknots with probknot . we restricted the size of helical regions in the final display to ≥4 base pairs and exported circle plots annotated with base-pair probabilities from the partition function. the 3d […]


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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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