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

Protein fold recognition by prediction-based threading

B Rost1, R Schneider, C Sander

  • 1EMBL, Heidelberg, Germany.

Journal of Molecular Biology
|July 18, 1997
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

Depressive and anxiety symptoms in individuals with Long-COVID: Does social network matter? - Results of a German Long-COVID study.

Journal of affective disorders·2026
Same author

Do values and political attitudes affect help-seeking? Exploring reported help-seeking for mental health problems in a general population sample using a milieu framework.

Epidemiology and psychiatric sciences·2023
Same author

Serum BDNF levels correlate with regional cortical thickness in minor depression: a pilot study.

Scientific reports·2020
Same author

Measurements of the associated production of a Z boson and b jets in pp collisions at <math> </math>.

The European physical journal. C, Particles and fields·2020
Same author

Resistance of Arctic phytoplankton to ocean acidification and enhanced irradiance.

Polar biology·2020
Same author

Study of Jet Quenching with Z+jet Correlations in Pb-Pb and pp Collisions at sqrt[s]_{NN}=5.02  TeV.

Physical review letters·2017
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

This study introduces a novel protein threading method that predicts secondary structure and solvent accessibility to evaluate sequence-structure fit. Surprisingly, this 1D profile approach achieves accuracy comparable to 3D methods for fold recognition.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Science

Background:

  • Protein threading is crucial for predicting 3D structures from amino acid sequences.
  • Current methods often rely on complex inter-residue potentials in 3D space.
  • Evaluating sequence-structure fitness remains a key challenge in bioinformatics.

Purpose of the Study:

  • To develop and evaluate an alternative protein threading method using predicted 1D structure profiles.
  • To compare the accuracy of this prediction-based threading approach against traditional 3D methods.
  • To investigate the effectiveness of 1D sequence-structure fitness evaluation for fold recognition.

Main Methods:

  • Predicting secondary structure and solvent accessibility for each amino acid residue.

Related Experiment Videos

  • Threading the resulting 1D profiles into known 3D protein structures using dynamic programming.
  • Fine-tuning the method with sequence-sequence comparison and empirical filters.

    • Main Results:

    • The prediction-based threading method demonstrates accuracy comparable to 3D interaction-based methods.
    • Structurally homologous regions were identified at first rank in 29% of cases.
    • Accurate fold recognition was achieved in 45-75% of first hits, outperforming fragment detection.

    Conclusions:

    • 1D structure profile threading is a viable and surprisingly effective alternative to 3D-based methods.
    • The method accurately predicts protein folds, suggesting 1D profiles capture essential fitness information.
    • This approach offers a computationally efficient strategy for protein structure prediction and fold recognition.