pKNOT protocols

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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 in pipeline

PMCID: 3705615
PMID: 23847399
DOI: 10.6026/97320630009456

[…] 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 []., the protein-protein docking simulation […]

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pKNOT in publications

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 […]

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

[…] 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 […]

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

[…] the protein is not able to find the native structure in all the attempted folding trajectories. such low folding efficiency is also apparent from the analysis of the probability of knot formation, pknot, as a function of nativeness. indeed, pknot increases abruptly from ∼0 to ∼1 only when the protein has more than 80% of its native contacts formed, showing that a highly compact conformation […]

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

[…] 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 […]

PMCID: 1904230
PMID: 17531098
DOI: 10.1186/1471-2199-8-44

[…] e. coli cells harboring phin also contained either pbr322 (pbr), which lacks recombination sites and serves as a negative control, or one of two pbr22-derived plasmids ptgse4 (prec) or prj862 (pknot) that carry sites recognized by the hin recombinase. all three plasmids contain the bla gene, which encodes β-lactamase and provides resistance to ampicillin. we used the bla gene as a reporter […]

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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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