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

Structure alignment via Delaunay tetrahedralization.

Jeffrey Roach1, Shantanu Sharma, Maryna Kapustina

  • 1Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA. roachjm@email.unc.edu

Proteins
|April 28, 2005
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

Beyond malaria prevention: sulfadoxine-pyrimethamine treatment in pregnancy selectively remodels the maternal gut microbiome to increase gestational weight gain and improve birthweight.

medRxiv : the preprint server for health sciences·2026
Same author

Comparative Effects of Therapeutic Exercise versus Muscle Energy Technique Combined with Transcutaneous Electrical Nerve Stimulation on Pain, Range of Motion, and Functional Outcomes after Anterior Cruciate Ligament Reconstruction: A Prospective Pilot Study.

Journal of orthopaedic case reports·2026
Same author

Unlocking the Effects of Neural Mobilization versus Transcutaneous Electrical Nerve Stimulation in Cervical Radiculopathy.

Journal of orthopaedic case reports·2026
Same author

A randomized controlled trial of probiotics to reduce the severity of oral mucositis in patients with oropharyngeal carcinoma undergoing concurrent chemoradiotherapy.

Journal of cancer research and therapeutics·2026
Same author

The low-density lipoprotein receptor LDLR mediates cellular entry of nonenveloped hepatitis A virus.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Association between Eating Disorders, Academic Stress with Menstrual Dysfunction among College Female Students: A Cross-Sectional Study.

Journal of lifestyle medicine·2026
Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026
Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026
Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026
Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026
Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026
Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
See all related articles

A new protein structure alignment method converts complex structures into a sequential representation, accelerating computations and revealing similarities missed by traditional techniques. This efficient approach aids genomic and evolutionary studies.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Structure Analysis

Background:

  • Traditional protein structure alignment methods often rely on rigid-body superposition, which may miss subtle structural similarities.
  • Accelerating structural computations is crucial for large-scale analyses in genomics and evolutionary biology.

Purpose of the Study:

  • To develop a novel protein structure alignment technique that enhances computational efficiency and uncovers non-superimposable structural similarities.
  • To complement existing methods by providing a complementary approach to protein structure comparison.

Main Methods:

  • Reducing protein secondary and tertiary structures to a sequential representation derived from Delaunay tetrahedralization.
  • Utilizing restricted alignments of the largest superimposable substructure for comparisons.

Related Experiment Videos

  • Applying principal component analysis to molecular dynamics snapshots for trajectory analysis.

    • Main Results:

    • The novel method achieved high accuracy in aligning histones and histone-like proteins, comparable to established tools like DaliLite and ProSup.
    • Demonstrated self-similarity in complex proteins (ferredoxin, cytidine deaminase, carbamoyl phosphate synthetase).
    • Achieved a 16-fold speedup in all-against-all similarity comparisons of aminoacyl-tRNA synthetases compared to distance matrix methods.
    • Revealed discrete protein microstates in tryptophanyl-tRNA synthetase trajectories via principal component analysis.

    Conclusions:

    • The developed technique significantly accelerates protein structure alignment and related computations.
    • It effectively identifies structural similarities not detectable by rigid-body superposition, complementing existing methods.
    • The method's efficiency and broad applicability make it suitable for large-scale genomic and evolutionary investigations.