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

Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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...
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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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 to...

You might also read

Related Articles

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

Sort by
Same author

Decoupling between activation time and steady-state level in input-output responses.

PLoS computational biology·2026
Same author

Lysosomal Profiling with LysoTracker for Quantitative Assessment of Cellular Senescence in Human Fibroblasts.

bioRxiv : the preprint server for biology·2026
Same author

Tolerance and growth outcomes in children diagnosed with cow's milk protein allergy and prescribed an extensively hydrolyzed casein formula (Damira 2000<sup>©</sup>) in Spain: The DELISA study.

Allergologia et immunopathologia·2026
Same author

Algebraic formulas for first-passage times of Markov processes in the linear framework.

Bulletin of mathematical biology·2025
Same author

Emergence of activation or repression in transcriptional control under a fixed molecular context.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

Decoupling between activation time and steady-state level in input-output responses.

bioRxiv : the preprint server for biology·2025
Same journal

Cross-Domain Transfer Learning from Peptides to Metabolites Using a Multi-Property Fine-Tuned LLM.

Bioinformatics (Oxford, England)·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: May 24, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Proteus: a web-based, context-specific modelling tool for molecular networks.

Florian Gnad1, Javier Estrada, Jeremy Gunawardena

  • 1Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.

Bioinformatics (Oxford, England)
|March 20, 2012
PubMed
Summary
This summary is machine-generated.

Proteus is a new web-based tool that allows researchers to rapidly build and explore context-specific mathematical models of molecular signaling pathways, such as calcium signaling, using ordinary differential equations (ODEs). This facilitates the integration of computational modeling with experimental data.

More Related Videos

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Related Experiment Videos

Last Updated: May 24, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Area of Science:

  • Systems Biology
  • Computational Biology
  • Molecular Signaling

Background:

  • Molecular networks are complex and context-specific.
  • Integrating computational modeling with experiments is challenging due to numerous modeling choices.
  • Exploring diverse modeling possibilities is time-consuming.

Purpose of the Study:

  • To develop a web-based tool, Proteus, for rapid construction and exploration of context-specific ordinary differential equation (ODE) models.
  • To facilitate the integration of computational modeling with experimental data in molecular systems biology.
  • To provide a flexible platform for building compartmentalized ODE models inspired by molecular toolkits.

Main Methods:

  • Developed Proteus, a web-based tool using a 'toolkit' approach for modular model building.
  • Users select context-independent components and mechanisms to define model specifics.
  • Proteus generates compartmentalized ODE models, exportable in SBML, Matlab, or Fortran formats.

Main Results:

  • Proteus enables rapid building, modification, and exploration of context-specific ODE models.
  • User-constructible toolkits, components, and mechanisms allow for model customization.
  • Models can be built de novo or by adapting existing models from databases like Biomodels.

Conclusions:

  • Proteus significantly accelerates the process of creating and analyzing context-specific molecular models.
  • The toolkit-based approach enhances the flexibility and reusability of modeling components.
  • This tool aids researchers in bridging the gap between computational modeling and experimental validation in systems biology.