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

Distance geometry based comparative modelling

A Aszódi1, R E Munro, W R Taylor

  • 1Division of Mathematical Biology, National Institute for Medical Research, London, UK.

Folding & Design
|January 1, 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

Can tibio-femoral kinematic and kinetic parameters reveal poor functionality and underlying deficits after total knee replacement? A systematic review.

The Knee·2021
Same author

In Vivo Elongation Patterns of the Collateral Ligaments in Healthy Knees During Functional Activities.

The Journal of bone and joint surgery. American volume·2021
Same author

The Matrilin-3 T298M mutation predisposes for post-traumatic osteoarthritis in a knock-in mouse model.

Osteoarthritis and cartilage·2020
Same author

Length-Change Patterns of the Collateral Ligaments During Functional Activities After Total Knee Arthroplasty.

Annals of biomedical engineering·2020
Same author

Author Correction: Tibio-Femoral Contact Force Distribution is Not the Only Factor Governing Pivot Location after Total Knee Arthroplasty.

Scientific reports·2019
Same author

Fiberoptic microindentation technique for early osteoarthritis diagnosis: an in vitro study on human cartilage.

Biomedical microdevices·2019
Same journal

Fishing for folding nuclei in lattice models and proteins.

Folding & design·1999
Same journal

Folding nucleus: specific or multiple? Insights from lattice models and experiments.

Folding & design·1999
Same journal

Sequential domain refolding of pig muscle 3-phosphoglycerate kinase: kinetic analysis of reactivation.

Folding & design·1999
Same journal

Discrete molecular dynamics studies of the folding of a protein-like model.

Folding & design·1999
Same journal

Knowledge-based structure prediction of MHC class I bound peptides: a study of 23 complexes.

Folding & design·1999
Same journal

How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains.

Folding & design·1999
See all related articles

This study introduces a distance geometry algorithm for protein modelling. It rapidly generates low-resolution models by projecting coordinates and using structural equivalences, serving as a basis for detailed refinement.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein modelling

Background:

  • Protein structure prediction is crucial for understanding function.
  • Existing methods may face challenges with speed and accuracy for novel protein targets.

Purpose of the Study:

  • To develop a novel distance geometry algorithm for efficient protein modelling.
  • To enable rapid generation of low-resolution models for further refinement.

Main Methods:

  • Utilizes distance geometry and projection into decreasing dimensionality Euclidean spaces.
  • Employs fast embedding via distance matrix projections on subsets.
  • Integrates structural equivalences from sequence/structure alignments or threading.
  • Applies conserved C-alpha distances and secondary structure restraints.

Related Experiment Videos

Main Results:

  • Successfully generated a large number of low-resolution protein models.
  • Demonstrated potential applications using 'Asilomar Challenge' (CASP2) targets.
  • The method provides viable starting conformations for full-atom refinement.

Conclusions:

  • The presented algorithm offers an efficient approach to protein structure prediction.
  • It effectively combines distance geometry with structural information for modelling.
  • The generated low-resolution models facilitate subsequent high-resolution structure determination.