pKNOT statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool pKNOT
info

Tool usage distribution map

This map represents all the scientific publications referring to pKNOT per scientific context
info info

Associated diseases

This word cloud represents pKNOT usage per disease context
info

Popular tool citations

chevron_left Knot prediction chevron_right
Want to access the full stats & trends on this tool?

Protocols

pKNOT specifications

Information


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

Maintainer


This tool is not available anymore.

Publications for pKNOT

pKNOT citations

 (7)
library_books

Proteins analysed as virtual knots

2017
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, […]

library_books

Network Properties of the Ensemble of RNA Structures

2015
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 […]

library_books

Knotted proteins: A tangled tale of Structural Biology

2015
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 […]

call_split

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

2013
Bioinformation
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) [http://nihserver.mbi.ucla.edu/SAVES/] and pKNOT v.2 web server [http://pknot.life.nctu.edu.tw/] were used for evaluation of the stereochemical qualities and protein knot in the modeled structures []. […]

library_books

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

2012
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 […]

library_books

On the combinatorics of sparsification

2012
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 […]


Want to access the full list of citations?
pKNOT institution(s)
Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan; Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan

pKNOT reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review pKNOT