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pKNOT specifications


Unique identifier OMICS_06175
Name pKNOT
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No


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Publications for pKNOT

pKNOT citations


Proteins analysed as virtual knots

Sci Rep
PMCID: 5304221
PMID: 28205562
DOI: 10.1038/srep42300

[…] in methodology, particularly in rare occasions where very severe chain breaks are present; 17 of our extra detections are considered knotted by one or both of the alternative protein knots databases pKNOT, or Protein Knots. We therefore consider that our sphere closure methodology accurately detects protein knotting for the purpose of comparison with virtual closure.In the sphere closure results, […]


Network Properties of the Ensemble of RNA Structures

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

[…] 6 Å, and that i, j are not consecutive (j ≠ i + 1). In , we consider several formulations of RNA contact order. The 3D absolute contact order for an RNA structure is defined as above. The pseudoknot (pknot) absolute contact order is defined as ∑i < j(j − i)/N, where the sum is over all N base pairs (i, j) determined by RNAview [], a program that determines hydrogen-bonded atoms of distinct nucleot […]


Knotted proteins: A tangled tale of Structural Biology

Comput Struct Biotechnol J
PMCID: 4556803
PMID: 26380658
DOI: 10.1016/j.csbj.2015.08.003

[…] a conformation is from the native one . The stage of the folding process at which knotting is more likely to occur can be inferred with high accuracy from the dependence of the knotting probability, pknot, on the reaction coordinate pfold . We found that knotting of our shallow trefoil knot occurs exceedingly late in folding, in conformations with pknot > 0.7 (a). An alternative, less computation […]


In silico analysis of caspase 3 and 7 proteases from blood parasitic Schistosoma species (Trematoda) and their human host

PMCID: 3705615
PMID: 23847399
DOI: 10.6026/97320630009456
call_split See protocol

[…] r4.0 Gromacs96 program [], respectively for getting more optimized and energetically favoured structures. Structure Analysis and Verification Server (SAVES) [] and pKNOT v.2 web server [] were used for evaluation of the stereochemical qualities and protein knot in the modeled structures []. […]


How Difficult Is It to Fold a Knotted Protein? In Silico Insights from Surface Tethered Folding Experiments

PLoS One
PMCID: 3527535
PMID: 23284997
DOI: 10.1371/journal.pone.0052343

[…] teins with trefoil knots. Indeed, we have noticed that the knotted core is located between 1 and 5 residues away from the C-terminus in the vast majority (74%) of the knotted trefoils reported in the pKNOT web server . Interestingly, in the remaining (few) cases, where the knotted core sits more deeply inside the protein sequence, it stays also closer to the C-terminus. Thus, our lattice system ca […]


On the combinatorics of sparsification

PMCID: 3549849
PMID: 23088372
DOI: 10.1186/1748-7188-7-28

[…] aining crossing arcs as pseudoknot structures.Generalizing the matrices of the DP-routines of secondary structure folding [,] to gap-matrices [], leads to a DP-folding of pseudoknotted structures [] (pknot‐R&E) with O(n4) space an O(n6) time complexity. The following references provide a certainly incomplete list of DP-approaches to RNA pseudoknot structure prediction using various structure class […]

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pKNOT institution(s)
Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan; Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan

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