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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
End Point Prediction: Gran Plot01:07

End Point Prediction: Gran Plot

A Gran plot is used to predict the equivalence volume or endpoint of a potentiometric or acid-base titration without reaching the endpoint. Typically, titration data is collected as a function of the titrant's volume up to a point less than the equivalence volume and then transformed into a linear format. The straight line is extended to the x-axis, indicating the necessary titrant volume to achieve the equivalence point.
For potentiometric titration, the Gran plot is created by plotting the...
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...

You might also read

Related Articles

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

Sort by
Same author

Heavy-chain immune repertoire sequencing enables language-model prediction of antigen-specific antibodies.

Research square·2026
Same author

Advances in Camptothecin-Class Compounds Nanomedicines: A Comprehensive Review of Antitumor Strategies.

Pharmaceutics·2026
Same author

Multimodal EHR-Based Prediction of Pediatric Asthma Exacerbations.

AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science·2026
Same author

A Curated Dataset for Question Answering on Laboratory Test Reference Ranges and Interpretation.

Scientific data·2026
Same author

When machines explain medicine: Nursing ethics and clinical communication.

Nursing ethics·2026
Same author

Chrysin reshapes ferroptosis sensitivity to reverse nickel refining fumes-induced lung injury via the miR-210/ANGPTL4 signaling axis mediated by the PHD1/HIF-1α pathway.

Ecotoxicology and environmental safety·2026
Same journal

CNV-ECOD: A copy number variation detection method based on ECOD algorithm using next-generation sequencing data.

Journal of bioinformatics and computational biology·2026
Same journal

ReinVar: A model-free paradigm-based reinforcement learning approach to detect copy number variation.

Journal of bioinformatics and computational biology·2026
Same journal

When pipelines run but coordinates fail: A simple spatial specificity check for false locality in post-GWAS analysis.

Journal of bioinformatics and computational biology·2026
Same journal

Comparative benchmarking of template-based, evolutionary-diffusion, and generative language models for IsPETase structure prediction.

Journal of bioinformatics and computational biology·2026
Same journal

Trap spaces as labelled ideals of SCC posets: A structural-functional theory of reachability in asynchronous boolean networks.

Journal of bioinformatics and computational biology·2026
Same journal

Erratum - DDINet: Drug-drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder.

Journal of bioinformatics and computational biology·2026
See all related articles

Related Experiment Video

Updated: Jun 27, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

A linear-time algorithm for predicting functional annotations from PPI networks.

Yonghui Wu1, Stefano Lonardi

  • 1Department of Computer Science and Engineering, University of California Riverside, Riverside, CA 92521, USA. yonghui@cs.ucr.edu

Journal of Bioinformatics and Computational Biology
|December 18, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces a new method to predict protein functions using protein-protein interaction (PPI) networks. The approach accurately predicts gene ontology (GO) annotations, outperforming existing techniques.

More Related Videos

Generalized Psychophysiological Interaction (PPI) Analysis of Memory Related Connectivity in Individuals at Genetic Risk for Alzheimer's Disease
09:38

Generalized Psychophysiological Interaction (PPI) Analysis of Memory Related Connectivity in Individuals at Genetic Risk for Alzheimer's Disease

Published on: November 14, 2017

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Related Experiment Videos

Last Updated: Jun 27, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Generalized Psychophysiological Interaction (PPI) Analysis of Memory Related Connectivity in Individuals at Genetic Risk for Alzheimer's Disease
09:38

Generalized Psychophysiological Interaction (PPI) Analysis of Memory Related Connectivity in Individuals at Genetic Risk for Alzheimer's Disease

Published on: November 14, 2017

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Systems Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Genome-wide, high-throughput protein-protein interaction (PPI) maps are now available for model organisms.
  • Analyzing these PPI networks is crucial for systems biology.
  • Predicting protein functions from network structure is a key challenge.

Purpose of the Study:

  • To develop a method for predicting protein functional classes (Gene Ontology annotations) using only PPI network structure.
  • To present a maximum likelihood formulation and associated algorithms for this prediction task.

Main Methods:

  • Developed a maximum likelihood formulation for predicting protein function from PPI networks.
  • Created learning and inference algorithms with linear time complexity relative to network size.

Main Results:

  • Experimental results demonstrate high accuracy in predicting protein functional classes.
  • The proposed method outperforms existing approaches for functional prediction based on PPI networks.

Conclusions:

  • The developed method offers an efficient and accurate way to predict protein functions from PPI network topology.
  • This work advances the field of systems biology by providing a powerful tool for functional annotation.