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,...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
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...

You might also read

Related Articles

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

Sort by
Same author

[Clinical Characteristics and Prognosis Analysis of MDS-RS Patients with Wild-Type <i>SF3B1</i>].

Zhongguo shi yan xue ye xue za zhi·2026
Same author

Corrigendum to "Recombinant OX40 attenuates neuronal apoptosis through OX40-OX40L/PI3K/AKT signaling pathway following subarachnoid hemorrhage in rats" [Experimental Neurology, 326 (2020), 113179-113,190/ PMID:31930990].

Experimental neurology·2026
Same author

Deficiency of Setd2 in mesenchymal stem cells facilitates the progression of myelodysplastic syndrome to leukemia.

Molecular medicine (Cambridge, Mass.)·2026
Same author

scSurvival: Single-Cell Survival Analysis of Clinical Cancer Cohort Data at Cellular Resolution.

Cancer discovery·2026
Same author

The mechanism study of isoorientin regulating neuroinflammation after subarachnoid hemorrhage through AKT/GSK3β.

International immunopharmacology·2026
Same author

Advancing spatial cellular communication inference with ligand diffusion and transport model.

Communications biology·2026

Related Experiment Video

Updated: Jul 9, 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

Predicting gene ontology functions from protein's regional surface structures.

Zhi-Ping Liu1, Ling-Yun Wu, Yong Wang

  • 1Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100080, China. zhiping.liu@hotmail.com

BMC Bioinformatics
|December 12, 2007
PubMed
Summary

Predicting protein functions is enhanced by analyzing pocket similarity networks. This method effectively links protein surface pockets to Gene Ontology (GO) functions, improving accuracy and efficiency.

More Related Videos

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Related Experiment Videos

Last Updated: Jul 9, 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

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein function annotation is crucial in the post-genomic era.
  • Traditional methods often overlook protein surface information, which is vital for biological interactions.
  • Databases like CASTp provide valuable structural surface data, including pockets and cavities.

Purpose of the Study:

  • To develop a novel method for predicting Gene Ontology (GO) functions of proteins.
  • To explore the relationship between protein pockets and their functions using network analysis.

Main Methods:

  • Construction of a pocket similarity network based on structural similarities of protein pockets.
  • Statistical analysis of network properties to correlate pocket similarity with GO functions.
  • Cross-validation experiments to evaluate prediction performance.

Main Results:

  • A novel method effectively predicts protein GO functions using pocket similarity networks.
  • The study reveals a strong relationship between protein surface pockets and GO functions.
  • The method demonstrates high computational efficiency and prediction accuracy.

Conclusions:

  • The pocket similarity network approach is effective for protein function prediction.
  • Protein pockets play essential roles in biological interactions and GO functions.
  • The network framework can be extended to utilize other protein surface patterns for function prediction.