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

Common Structural Cliques: a tool for protein structure and function analysis.

Mariusz Milik1, Sándor Szalma, Krzysztof A Olszewski

  • 1Accelrys, 9685 Scranton Road, San Diego, CA 92121, USA.

Protein Engineering
|September 12, 2003
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

Crystal structure, thermostability and temperature-dependent enzymatic activity of an exo-β-d-glucosaminidase from Pyrococcus chitonophagus.

Journal of structural biology·2026
Same author

Correction: Assessing the potential of polygenic scores to strengthen medical risk prediction models of COVID-19.

PloS one·2025
Same author

Correction: Mapping of UK Biobank clinical codes: Challenges and possible solutions.

PloS one·2024
Same author

Investigation of genetic determinants of cognitive change in later life.

Translational psychiatry·2024
Same author

Plasma proteomic associations with genetics and health in the UK Biobank.

Nature·2023
Same author

Assessing the potential of polygenic scores to strengthen medical risk prediction models of COVID-19.

PloS one·2023
Same journal

Structure of a human Rhinovirus complexed with its receptor molecule.

Protein engineering·2024
Same journal

pH-responsive polymer-assisted refolding of urea- and organic solvent-denatured alpha-chymotrypsin.

Protein engineering·2004
Same journal

Evaluation of different linker regions for multimerization and coupling chemistry for immobilization of a proteinaceous affinity ligand.

Protein engineering·2004
Same journal

Recombinant porcine intestinal carboxylesterase: cloning from the pig liver esterase gene by site-directed mutagenesis, functional expression and characterization.

Protein engineering·2004
Same journal

Periplasmic expression of human growth hormone via plasmid vectors containing the lambdaPL promoter: use of HPLC for product quantification.

Protein engineering·2004
Same journal

Shift of fibril-forming ability of the designed alpha-helical coiled-coil peptides into the physiological pH region.

Protein engineering·2004
See all related articles

This study introduces a novel method to identify key atoms in protein structures by comparing local features, regardless of overall similarity. This approach effectively reveals common structural templates for proteins with shared functions, even those with different evolutionary origins.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Identifying functionally relevant atoms in proteins is crucial for understanding biochemical mechanisms.
  • Existing methods often rely on sequence or overall structural similarity, limiting their scope.
  • A flexible representation of protein active sites is needed to capture diverse functional arrangements.

Purpose of the Study:

  • To propose a novel method for locating functionally relevant atoms in protein structures.
  • To develop a flexible representation of spatial arrangements for protein active sites.
  • To enable the discovery of functional analogies between proteins based on local structural features.

Main Methods:

  • Proteins are represented as graphs with atoms as nodes and distances as edge labels.

Related Experiment Videos

  • A search method compares local structural features of proteins sharing common biochemical functions.
  • Common Structural Cliques are extracted and merged to create Structural Templates.

    • Main Results:

    • The method successfully identified common structural features in serine endopeptidases and aminotransferases.
    • It efficiently handles large protein systems and does not require prior knowledge of functionally relevant residues.
    • Structural Templates effectively capture analogies between proteins, even those with convergent evolution.

    Conclusions:

    • The proposed method provides an efficient way to locate functionally relevant atoms and describe protein active sites flexibly.
    • It successfully extracts common structural features from proteins with shared functions, irrespective of sequence or overall structure similarity.
    • This approach is valuable for studying protein families, especially those shaped by convergent evolution.