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-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...
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,...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

You might also read

Related Articles

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

Sort by
Same author

NECAP antagonizes light-induced Rhodopsin-1 internalization to promote photoreceptor homeostasis.

bioRxiv : the preprint server for biology·2026
Same author

Conserved principles of central carbon partitioning in Hippo-Yorkie-driven <i>Drosophila</i> gut tumors.

bioRxiv : the preprint server for biology·2026
Same author

Genome-wide CRISPR knockout cell screening platform for the disease vector tick species <i>Ixodes scapularis</i>.

bioRxiv : the preprint server for biology·2026
Same author

Author Correction: Streptomyces produce a diphtheria toxin-like exotoxin that targets insects.

Nature microbiology·2026
Same author

Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci.

bioRxiv : the preprint server for biology·2026
Same author

Streptomyces produce a diphtheria toxin-like exotoxin that targets insects.

Nature microbiology·2026
Same journal

Complex Indel Detection: A Simulation-Based Framework and Parsing with FreeBayes.

bioRxiv : the preprint server for biology·2026
Same journal

Emulating the gingival-tooth interface during bacterial, fungal, and viral infection in a microphysiological model of the human oral cavity.

bioRxiv : the preprint server for biology·2026
Same journal

Local SNP-explained methylation variation reveals genetically anchored and exposure-associated methylation architecture in the human brain.

bioRxiv : the preprint server for biology·2026
Same journal

Perinatal Semaglutide Treatment Improves Maternal Health and Mitigates Offspring Metabolic Dysfunction in a Mouse Model of Maternal Obesity.

bioRxiv : the preprint server for biology·2026
Same journal

Pervasive cryptic selection in the human noncoding genome.

bioRxiv : the preprint server for biology·2026
Same journal

Secreted ORF8 reprograms macrophages to enhance SARS-CoV-2 infection of lung epithelial cells.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: May 19, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

LIVIA: a browser-based tool for assessing and visualizing predicted protein interactions.

Ah-Ram Kim1, Norbert Perrimon1,2

  • 1Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.

Biorxiv : the Preprint Server for Biology
|May 18, 2026
PubMed
Summary
This summary is machine-generated.

LIVIA is a new tool for visualizing protein-protein interactions (PPIs). It assesses interaction confidence and identifies key residues, making complex biological data more accessible for researchers.

More Related Videos

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
11:19

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Related Experiment Videos

Last Updated: May 19, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
11:19

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • Protein structure prediction tools are increasingly used in biological research.
  • Assessing and visualizing predicted protein-protein interactions (PPIs) remains a challenge.
  • There is a need for user-friendly methods to analyze PPI data from various prediction platforms.

Purpose of the Study:

  • To introduce LIVIA (Local Interaction Visualization and Analysis), a novel browser-based tool.
  • To provide accessible methods for assessing and visualizing predicted PPIs.
  • To facilitate the identification of interface residues and confidence metrics for PPIs.

Main Methods:

  • LIVIA computes local PPI confidence metrics by integrating data from multiple prediction platforms.
  • The tool automatically detects and parses various prediction file formats.
  • It identifies predicted interface residues and embeds an interactive Mol* 3D viewer for local analysis.
  • LIVIA generates visualization scripts compatible with ChimeraX and PyMOL.

Main Results:

  • LIVIA offers a unified approach to analyze PPI predictions from diverse sources.
  • The tool enables local computation, ensuring user data privacy and security.
  • It provides interactive visualization of PPIs and identification of critical interface residues.
  • Generated scripts allow for high-quality visualization in established molecular graphics software.

Conclusions:

  • LIVIA enhances the accessibility and interpretability of predicted protein-protein interactions.
  • The tool empowers researchers to critically evaluate and visualize PPI data.
  • LIVIA supports the advancement of structural biology and drug discovery through improved PPI analysis.