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

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
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 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

Functional Analysis of MS-Based Proteomics Data: From Protein Groups to Networks.

Molecular & cellular proteomics : MCP·2024
Same author

Biomedical knowledge graph-optimized prompt generation for large language models.

Bioinformatics (Oxford, England)·2024
Same author

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX.

Acta crystallographica. Section D, Structural biology·2024
Same author

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.

Journal of molecular biology·2024
Same author

UCSF ChimeraX: Tools for structure building and analysis.

Protein science : a publication of the Protein Society·2023
Same author

Translating desktop success to the web in the cytoscape project.

Frontiers in bioinformatics·2023

Related Experiment Video

Updated: Jun 12, 2026

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

Computational tools for the interactive exploration of proteomic and structural data.

John H Morris1, Elaine C Meng, Thomas E Ferrin

  • 1Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA.

Molecular & Cellular Proteomics : MCP
|June 8, 2010
PubMed
Summary
This summary is machine-generated.

Interactive tools are needed to link proteomics and structural data for cellular process research. This study presents two such computational tools to aid hypothesis development and confirmation in silico.

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

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

Related Experiment Videos

Last Updated: Jun 12, 2026

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

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

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

Area of Science:

  • Proteomics
  • Structural Biology
  • Computational Biology

Background:

  • Understanding cellular processes requires integrating proteomics and structural data.
  • Interactive exploration of these complementary datasets aids hypothesis generation and validation.
  • Existing computational tools for integrated data exploration are not widely understood or utilized.

Purpose of the Study:

  • To address the need for effective tools linking proteomics and structural data.
  • To present two specific computational tools for integrated data exploration.
  • To demonstrate the utility of these tools through practical scenarios.

Main Methods:

  • Review of existing computational tools for integrating proteomics and structural data.
  • In-depth presentation of two selected tools.
  • Illustrative scenarios showcasing integrated data exploration.

Main Results:

  • Identification of a gap in accessible, interactive tools for combined proteomics and structural data analysis.
  • Detailed exposition of two distinct computational tools designed for this purpose.
  • Demonstration of the practical application of these tools in biological research contexts.

Conclusions:

  • Effective integration of proteomics and structural data is crucial for advancing biological understanding.
  • The presented tools offer valuable solutions for interactive, in silico hypothesis testing.
  • Increased adoption of such integrated tools can accelerate discoveries in proteomics and structural biology.