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

4.7K
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,...
4.7K
Protein Networks02:26

Protein Networks

2.9K
2.9K
Protein-protein Interfaces02:04

Protein-protein Interfaces

15.0K
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...
15.0K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

4.6K
4.6K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

3.0K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
3.0K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.2K
2.2K

You might also read

Related Articles

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

Sort by
Same author

On the state of protein function prediction: a report on the fourth CAFA challenge.

bioRxiv : the preprint server for biology·2026
Same author

Advances in Protein Function Prediction from the Fifth CAFA Challenge.

bioRxiv : the preprint server for biology·2026
Same author

Open and sustainable AI: challenges, opportunities and the road ahead in the life sciences.

Nature methods·2026
Same author

Exploring proteins and protein-ligand complexes through residue interaction networks.

Nature protocols·2026
Same author

Effects of Mutations on Tandem-Repeat Proteins Conformation Mechanisms. Application to the Phosphatase PP2A.

Journal of chemical information and modeling·2026
Same author

Toward a unified framework for determining conformational ensembles of disordered proteins.

Nature methods·2026

Related Experiment Video

Updated: Mar 21, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K

The RING 2.0 web server for high quality residue interaction networks.

Damiano Piovesan1, Giovanni Minervini1, Silvio C E Tosatto2

  • 1Department of Biomedical Sciences, University of Padua, Padua 35121, Italy.

Nucleic Acids Research
|May 21, 2016
PubMed
Summary

The updated RING 2.0 software rapidly identifies covalent and non-covalent interactions in protein structures, creating residue interaction networks (RINs) for detailed structural analysis and visualization.

More Related Videos

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

1.3K
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

17.2K

Related Experiment Videos

Last Updated: Mar 21, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K
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

1.3K
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

17.2K

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Chemistry

Background:

  • Residue Interaction Networks (RINs) represent protein structures as graphs of interacting residues.
  • RINs are valuable for analyzing protein folding, mutation effects, and catalytic activity.
  • Existing tools require improvement for comprehensive interaction identification.

Purpose of the Study:

  • Introduce RING 2.0, an enhanced software for identifying protein residue interactions.
  • Improve the speed and accuracy of generating residue interaction networks.
  • Provide advanced visualization tools for protein structural analysis.

Main Methods:

  • Developed RING 2.0, a software for identifying covalent and non-covalent bonds, including π-π stacking and π-cation interactions.
  • Utilized empirical re-parameterization of distance thresholds across the Protein Data Bank for accuracy.
  • Integrated web server and RING-Viz script for customizable calculations and atomic-level visualization.

Main Results:

  • RING 2.0 achieves high speed and accuracy in generating intra- and inter-chain interactions, including solvent and ligand atoms.
  • The software reliably identifies a wide range of physico-chemical interactions within protein structures.
  • Generated networks are visualized directly in browsers, Cytoscape, or at the atomic level using RING-Viz for PyMOL.

Conclusions:

  • RING 2.0 offers a fast, accurate, and versatile platform for generating and analyzing residue interaction networks.
  • The enhanced capabilities facilitate deeper insights into protein structure-function relationships.
  • Accessible web server and visualization tools support broad application in structural biology research.