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 Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Monoterpenoid-ciprofloxacin hybrids as a strategy to disrupt Staphylococcus aureus biofilms and overcome associated resistance.

Journal of advanced research·2026
Same author

Tolcapone-loaded nanostructured lipid carriers for improved oral delivery.

International journal of pharmaceutics·2026
Same author

Chromones as Nonclassical Inhibitors of Carbonic Anhydrase IX and XII Isoforms: Probing Chromone-Based Derivatives.

Archiv der Pharmazie·2026
Same author

Hydroxycinnamic and Hydroxybenzoic-Based Mitochondriotropic Antioxidants Improve Bovine Embryo Quality and Cryo-Survival.

Veterinary sciences·2026
Same author

25-nitro-20-epi-vitamin D analogue with anti-proliferative and cytoprotective properties: Biological and pharmacological evaluation.

Experimental and molecular pathology·2026
Same author

Mitochondria-targeted antioxidant AntiOxBEN<sub>2</sub> prevents metabolic dysfunction-associated steatotic liver disease (MASLD) by enhancing fatty acid oxidation and mitochondrial bioenergetics.

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie·2026

Related Experiment Video

Updated: Jul 2, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Natural/random protein classification models based on star network topological indices.

Cristian Robert Munteanu1, Humberto González-Díaz, Fernanda Borges

  • 1REQUIMTE-University of Porto, Faculty of Science, Chemistry Department, University of Porto 4169-007, Portugal. muntisa@gmail.com

Journal of Theoretical Biology
|August 12, 2008
PubMed
Summary

This study introduces a novel method using star network topological indices to classify protein sequences as natural or random. The Sequence to Star Networks (S2SNet) application achieves high accuracy, aiding in protein function studies and error detection.

More Related Videos

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Related Experiment Videos

Last Updated: Jul 2, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Network Science

Background:

  • Complex network graphs are used to model real-world systems by converting properties into topological indices (TIs).
  • Protein primary structure data can be transformed into TIs for classification models.
  • Randic's star networks offer a framework for this transformation.

Purpose of the Study:

  • To develop a model for classifying protein sequences as natural or random using star network topological indices.
  • To introduce the Sequence to Star Networks (S2SNet) application for this purpose.
  • To extend the application of TIs to protein sequence analysis.

Main Methods:

  • Utilized 1046 natural protein chains (CulledPDB, 20% homology, 1.6Å resolution, R-factor < 25%) and 1046 generated random amino acid chains.
  • Developed the Sequence to Star Networks (S2SNet) GUI application with a Graphviz back-end.
  • Calculated various star network topological indices including Shannon entropy, Harary number, Wiener index, and connectivity indices.

Main Results:

  • The S2SNet application successfully converted protein sequences into topological indices.
  • A classification model built using General Discriminant Analysis achieved 90.77% accuracy on training and prediction sets.
  • The model demonstrated the ability to distinguish between natural and random protein sequences based solely on amino acid sequence data.

Conclusions:

  • This study pioneers the use of protein star network topological indices for classifying protein sequences.
  • The developed model and S2SNet application can predict if a protein or fragment is natural or random.
  • Applications include protein function studies, detection of artificial sequences, and error identification in proteomics and imaging.