Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

pKNOT: the protein KNOT web server.

Yan-Long Lai1, Shih-Chung Yen, Sung-Huan Yu

  • 1Institute of Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan.

Nucleic Acids Research
|May 29, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Identification and biological evaluation of benzimidazole-based compounds as novel TGFβR1 inhibitors.

Journal of enzyme inhibition and medicinal chemistry·2026
Same author

Consensus Pharmacological Interactions for PLK2 Inhibitor Identification in Colorectal Cancer Treatment.

Journal of chemical information and modeling·2025
Same author

Semi-inductive dataset construction and framework optimization for practical drug target interaction prediction with ScopeDTI.

Nature communications·2025
Same author

Exploring diarylheptanoid derivatives to target LIMK1 as potential agents against colorectal cancer.

Journal of enzyme inhibition and medicinal chemistry·2025
Same author

AlphaPPIweb: an integration platform for protein-protein interaction prediction and evaluation.

American journal of cancer research·2025
Same author

SARST2 high-throughput and resource-efficient protein structure alignment against massive databases.

Nature communications·2025
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

The protein KNOT (pKNOT) web server is the first tool to identify knotted proteins in the Protein Data Bank (PDB). This resource aids biologists in accurately detecting and visualizing protein knots, improving structural biology research.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Knotted proteins are increasingly identified in the Protein Data Bank (PDB).
  • Knot regions are implicated in crucial protein functions like ligand binding and enzyme activity.
  • A lack of accessible tools leads to misidentification of protein knots in scientific literature.

Purpose of the Study:

  • To introduce the protein KNOT (pKNOT) web server, the first dedicated tool for detecting knots in proteins.
  • To provide a user-friendly platform for biologists to identify and analyze knotted proteins within the PDB.
  • To facilitate accurate knot identification and visualization, reducing errors in published research.

Main Methods:

  • Users can submit protein structures via PDB ID or by uploading PDB coordinate files.

Related Experiment Videos

  • The pKNOT server employs Taylor's smoothing algorithm for knot detection.
  • Detected knots are visualized using an integrated Java-based 3D graphics viewer.

    • Main Results:

    • The pKNOT web server successfully detects knots in protein structures.
    • It provides a visual inspection capability for identified knots.
    • The server offers a centralized resource for information on knotted proteins in the PDB.

    Conclusions:

    • The pKNOT web server addresses the need for a reliable tool for protein knot identification.
    • This resource is expected to benefit general biologists and structural biologists by improving accuracy and accessibility.
    • pKNOT aims to enhance the study of knotted proteins and their functional significance.