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

Decoy models for protein structure comparison score normalisation.

William R Taylor1

  • 1Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. wtaylor@nimr.mrc.ac.uk

Journal of Molecular Biology
|February 7, 2006
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

Immediate and Mid-Long-Term Effects of Foot Orthoses on Gait Biomechanics and Clinical Characteristics in Medial Knee Osteoarthritis: A Systematic Review and Meta-analysis.

Annals of biomedical engineering·2026
Same author

Advancing Conservative Treatment of Knee Osteoarthritis: 3D-Printed Shoe Soles for Passive Toe-Out Gait Modification.

Journal of foot and ankle research·2026
Same author

Pose-aware deep perceptual similarity for iterative 2D/3D registration of knee joints using contrastive learning.

International journal of computer assisted radiology and surgery·2026
Same author

Passive Laxity in Patients With Subjective Instability Following a Cruciate-Retaining Total Knee Arthroplasty: A Pilot Study.

JB & JS open access·2026
Same author

Enhanced Molecular Staging of Pancreatic Cancer Using Methylated DNA Markers in Peritoneal Lavage Fluid.

Journal of surgical oncology·2026
Same author

Can we identify which patients are likely to have septic arthritis with borderline synovial fluid cell counts?

Journal of bone and joint infection·2026

A new method generates decoy protein models for accurate structure comparison. This approach ensures reliable background score distributions, improving the assessment of protein fold similarities and differences.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure analysis

Background:

  • Protein structure comparison is crucial for understanding protein function and evolution.
  • Existing methods for generating background score distributions can be complex and require normalization.
  • Accurate comparison necessitates methods that account for structural properties while differentiating folds.

Purpose of the Study:

  • To develop a novel method for constructing decoy models for protein structure comparison.
  • To establish a robust background score distribution for evaluating structural similarities.
  • To enable accurate comparison of proteins, including substructure and domain matches, and facilitate joint family/family comparisons.

Main Methods:

  • Decoy models are generated directly from the proteins being compared.

Related Experiment Videos

  • Decoy models retain essential structural properties: length, density, shape, and secondary structure composition.
  • The method inherently handles proteins of the same length, eliminating the need for explicit length normalization.

    • Main Results:

    • The described method produces decoy models with different folds but preserved structural characteristics.
    • Substructure and domain matches are scored comparably to isolated domain comparisons.
    • A normalized probability measure was derived, enabling effective joint family/family comparisons.
    • The method was successfully applied to CASP6 models, including targets with novel folds.

    Conclusions:

    • The developed method provides a reliable way to generate background score distributions for protein structure comparison.
    • This approach simplifies comparisons by avoiding explicit length normalization and allows for nuanced assessment of structural similarity.
    • The technique is effective for comparing proteins of various complexities, including those with new folds, as demonstrated in CASP6.