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

Visual System01:26

Visual System

1.8K
Light enters the eye through the cornea, a transparent, dome-shaped surface covering the surface of the eyeball that helps to direct and focus incoming light. This light is then channeled toward the pupil, an adjustable opening whose size is controlled by the iris. The iris, a pigmented muscle, regulates the amount of light entering the eye by contracting or dilating the pupil, thereby ensuring optimal light levels for clear vision.
Once through the pupil, the light passes through the lens, a...
1.8K
Overview of Microsoft Excel as a Data Analysis Tool01:13

Overview of Microsoft Excel as a Data Analysis Tool

1.6K
Microsoft Excel is a cornerstone tool for data analysis and statistical operations, offering a wide array of functionalities to manage, analyze, and visualize data efficiently. Recognized for its versatility, Excel facilitates the performance of basic to complex statistical operations, serving as an indispensable asset for analysts, researchers, and students alike. Excel's significance in data analysis emanates from its spreadsheet environment, where data can be organized in rows and...
1.6K
Visual Agnosia01:12

Visual Agnosia

1.1K
Visual agnosia is a condition characterized by the inability to recognize visually presented objects despite having normal vision. For instance, a person with visual agnosia can describe the shape and color of an object but cannot identify or name it. This impairment does not affect their visual field, acuity, color vision, brightness discrimination, language, or memory. An example of this condition in a social setting is someone at a dinner party asking for "that silver thing with a round...
1.1K
Photoreceptors and Visual Pathways01:22

Photoreceptors and Visual Pathways

9.2K
At the molecular level, visual signals trigger transformations in photopigment molecules, resulting in changes in the photoreceptor cell's membrane potential. The photon's energy level is denoted by its wavelength, with each specific wavelength of visible light associated with a distinct color. The spectral range of visible light, classified as electromagnetic radiation, spans from 380 to 720 nm. Electromagnetic radiation wavelengths exceeding 720 nm fall under the infrared category,...
9.2K
Molecular Shapes01:18

Molecular Shapes

62.0K
Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
62.0K
Protein Networks02:26

Protein Networks

4.5K
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,...
4.5K

You might also read

Related Articles

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

Sort by
Same author

Scaling Up Task-Shared Depression Care in Texas: Evaluating the Preliminary Effectiveness and Acceptability of a Digital Program for Training Non-Specialist Providers.

Psychiatric research and clinical practice·2026
Same author

Site Confidence Scores among All Available Structures to Help Infer Conformational Origins of Identified Cross-Links.

Journal of proteome research·2026
Same author

On the Feasibility of Clinical Studies with Cross-Linking Mass Spectrometry.

Journal of proteome research·2026
Same author

Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing.

Journal of proteome research·2025
Same author

Open-Source and FAIR Research Software for Proteomics.

Journal of proteome research·2025
Same author

Neoadjuvant chemotherapy with bevacizumab for locally advanced vulvar cancer.

International journal of gynecological cancer : official journal of the International Gynecological Cancer Society·2025
Same journal

Proteomic Profiling of Extracellular Vesicle-Enriched Plasma Using Mag-Net for Biomarker Discovery in Pancreatic Ductal Adenocarcinoma.

Journal of proteome research·2026
Same journal

Computationally Efficient Bayesian Estimation of Graphical Networks for Omics Data.

Journal of proteome research·2026
Same journal

Hierarchy of MS-Based Evidence.

Journal of proteome research·2026
Same journal

Proteomic Profiling of Exosomes from HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinoma: Selective Cargo Packaging.

Journal of proteome research·2026
Same journal

Proteomic Analysis Identifies ATE1-Dependent Arginylation Dysregulation across Meningioma Grades.

Journal of proteome research·2026
Same journal

Proteomic Impact of Peripheral Expression of Mutant Huntingtin in <i>C. elegans</i>.

Journal of proteome research·2026
See all related articles

Related Experiment Video

Updated: Feb 1, 2026

mRNA Interactome Capture from Plant Protoplasts
12:29

mRNA Interactome Capture from Plant Protoplasts

Published on: July 28, 2017

9.6K

Tools for 3D Interactome Visualization.

Andrew Keller1, Juan D Chavez1, Jimmy K Eng1

  • 1Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States.

Journal of Proteome Research
|December 7, 2018
PubMed
Summary
This summary is machine-generated.

New informatics tools visualize dynamic protein interactome changes revealed by quantitative cross-linking and mass spectrometry (XL-MS). This 3D visualization aids understanding of cellular responses to various perturbations.

Keywords:
cross-link databasecross-linkingdynamic interactomeheatmapinteraction surfacesinteractome moviesmass spectrometryprotein complexesprotein interaction networksquantitative proteomics

More Related Videos

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
11:29

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

12.3K
3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells
11:25

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells

Published on: January 25, 2020

10.9K

Related Experiment Videos

Last Updated: Feb 1, 2026

mRNA Interactome Capture from Plant Protoplasts
12:29

mRNA Interactome Capture from Plant Protoplasts

Published on: July 28, 2017

9.6K
Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
11:29

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

12.3K
3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells
11:25

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells

Published on: January 25, 2020

10.9K

Area of Science:

  • Biochemistry
  • Cell Biology
  • Bioinformatics

Background:

  • Protein interactions (interactome) are crucial for cellular function and dynamic modulation.
  • Cross-linking and mass spectrometry (XL-MS) detect protein interactions within biological systems.
  • Quantitative XL-MS measures interactome changes in response to perturbations.

Purpose of the Study:

  • To develop novel informatics tools for 3D visualization of dynamic interactome data.
  • To integrate these tools into the XLinkDB database and analysis suite.
  • To address the growing need for advanced visualization in quantitative XL-MS studies.

Main Methods:

  • Development of new informatics capabilities for 3D interactome visualization.
  • Integration of visualization tools into XLinkDB release 3.0.
  • Application to multiple quantitative XL-MS datasets over time or with varied perturbations.

Main Results:

  • First-in-class 3D visualization of multiple quantitative interactome datasets.
  • Revealed dynamic interactome changes under different conditions.
  • Enhanced analysis capabilities within the XLinkDB platform.

Conclusions:

  • The developed 3D visualization tools are essential for interpreting complex quantitative XL-MS data.
  • These tools facilitate a deeper understanding of dynamic cellular processes and responses.
  • XLinkDB 3.0 provides a comprehensive platform for interactome analysis and visualization.