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

Three-dimensional structure analysis of PROSITE patterns.

A Kasuya1, J M Thornton

  • 1Department of Biochemistry & Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.

Journal of Molecular Biology
|March 5, 1999
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

Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.

Journal of cheminformatics·2024
Same author

Resolvin D2 promotes host defense in a 2 - hit model of sepsis with secondary lung infection.

Prostaglandins & other lipid mediators·2022
Same author

Lipoxin A4 promotes reduction and antibiotic efficacy against Pseudomonas aeruginosa biofilm.

Prostaglandins & other lipid mediators·2020
Same author

Multiple facial plaques of diffuse plane xanthoma arising from regressed tumours of folliculotropic mycosis fungoides.

Clinical and experimental dermatology·2020
Same author

Capsule-like naevus: digital 3D reconstruction of its steric structure.

Journal of the European Academy of Dermatology and Venereology : JEADV·2019
Same author

Digitally reconstructed top-down view images provide intuitive understanding of the correlation between dermoscopy and histopathology: a good educational tool.

The British journal of dermatology·2019
Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026
Same journal

Antibody-secreting cells integrate efficient NMD with non‑canonical UPR signaling to maintain proteostasis and support massive immunoglobulin synthesis.

Journal of molecular biology·2026
Same journal

Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry.

Journal of molecular biology·2026
Same journal

UPF1 at Work: Structural and Mechanistic Insights Into a Master Regulator of Nonsense-Mediated mRNA Decay.

Journal of molecular biology·2026
Same journal

Structural basis for the pro-amyloidogenic action and ligand binding of a novel W72R variant of human apolipoprotein A-I.

Journal of molecular biology·2026
Same journal

Cryo-EM Structure of the C. elegans Septin Tetramer Reveals a Revised Architecture and Conserved Positional Orthology.

Journal of molecular biology·2026
See all related articles

Searching protein sequences in the Protein Data Bank (PDB) revealed that true pattern matches share common 3D structures. This finding could enable the creation of 3D functional patterns for protein analysis.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • PROSITE database contains sequence patterns for protein families.
  • Protein Data Bank (PDB) archives protein 3D structures.
  • Distinguishing true functional patterns from false positives is crucial.

Purpose of the Study:

  • To investigate if true pattern matches in protein sequences exhibit common three-dimensional (3D) structures.
  • To determine if false positive pattern matches have distinct 3D structures.
  • To explore the potential for defining 3D functional patterns.

Main Methods:

  • Searched PROSITE sequence patterns against all protein sequences in the PDB.
  • Analyzed the 3D structures of pattern matches for the 20 most frequent patterns.

Related Experiment Videos

  • Compared the 3D structures of true positives and false positives.

    • Main Results:

    • True positives for each pattern consistently showed a common 3D structure.
    • False positives, identified for six patterns, displayed significantly different 3D structures compared to true positives.
    • A clear structural distinction exists between true and false pattern matches.

    Conclusions:

    • True sequence pattern matches possess characteristic, common 3D structures.
    • These common 3D structures can serve as templates for defining 3D functional patterns.
    • Structural analysis of pattern matches offers a method to improve pattern accuracy and functional prediction.