Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Coupled Reactions

Coupled Reactions

Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Cells often couple the energy-releasing reaction with the energy-requiring one to carry out important cell functions.
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions. Cells...

Molecular Models

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.

GPCRs Regulate Adenylyl Cylase Activity

GPCRs Regulate Adenylyl Cylase Activity

Some GPCRs transmit signals through adenylyl cyclase (AC), a transmembrane enzyme. AC helps synthesize second messenger cyclic adenosine monophosphate (cAMP). AC catalyzes cyclization reaction and converts ATP to cAMP by releasing a pyrophosphate. The pyrophosphate is further hydrolyzed to phosphate by the enzyme pyrophosphatase, which drives cAMP synthesis to completion. However, cAMP is rapidly degraded to 5′ AMP by the enzymes phosphodiesterase (PDE), preventing overstimulation of cells.
Two...

Calmodulin-dependent Signaling

Calmodulin-dependent Signaling

Calmodulin (CaM) is a calcium-binding protein in eukaryotes that controls various calcium-regulated cellular processes. It has four calcium-binding sites that bind calcium to form the calcium-calmodulin ( Ca2+-CaM) complex. GPCR stimulation increases the calcium levels in the cells that bind to CaM and induces a conformational change.
The Ca2+-CaM complex does not have enzymatic activity by itself. Instead, the complex binds downstream target proteins, including membrane proteins or enzymes,...

You might also read

Related Articles

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

Sort by

Same author

Correction to 'Control and regulation of pathways via negative feedback'.

Journal of the Royal Society, Interface·2017

Same author

Mathematical modeling and synthetic biology.

Drug discovery today. Disease models·2016

Same author

From patient-specific mathematical neuro-oncology to precision medicine.

Frontiers in oncology·2013

Same author

In silico evolution of functional modules in biochemical networks.

Systems biology·2006

Same author

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Bioinformatics (Oxford, England)·2003

Same author

Increased expression of NOS and ET-1 immunoreactivity in human colorectal metastatic liver tumours is associated with selective depression of constitutive NOS immunoreactivity in vessel endothelium.

Journal of submicroscopic cytology and pathology·2002

Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026

Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026

Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026

Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026

Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026

Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 7, 2026

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

A C library for retrieving specific reactions from the BioModels database.

M L Neal¹, M Galdzicki, J T Gallimore

¹Department of Bioengineering, University of Washington, Seattle, WA 98195, USA and Department of Computer Science, Wofford College, Spartanburg, SC 29303, USA.

Bioinformatics (Oxford, England)

|October 1, 2013

Summary

This summary is machine-generated.

libSBMLReactionFinder is a new C library that helps systems biologists find specific biochemical reactions in the BioModels database. This tool accelerates modeling by enabling easy retrieval of reactions using text searches.

More Related Videos

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Related Experiment Videos

Last Updated: May 7, 2026

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Area of Science:

Systems Biology
Computational Biology
Biochemistry

Background:

The BioModels database contains curated Systems Biology Markup Language (SBML) models.
Accessing specific biochemical reactions within these models can be challenging for researchers.
Efficient retrieval of reaction data is crucial for quantitative modeling and hypothesis testing.

Purpose of the Study:

To develop a C library, libSBMLReactionFinder, for efficiently retrieving biochemical reactions from the BioModels database.
To enable users to find reactions using simple string searches based on semantic annotations.
To accelerate quantitative modeling efforts by facilitating the reuse of existing reaction representations.

Main Methods:

Developed a C library, libSBMLReactionFinder.
Leveraged semantic annotations within the BioModels database.
Implemented a search functionality based on human-readable descriptions associated with reactions.

Main Results:

libSBMLReactionFinder allows retrieval of specific biochemical reactions from SBML models.
Semantic annotations are used to link reactions to descriptive text.
Reactions are made searchable via simple string queries.

Conclusions:

libSBMLReactionFinder provides a valuable tool for quantitative modelers.
The library simplifies and accelerates the process of finding and reusing biochemical reactions.
This facilitates the advancement of systems biology research through efficient model component reuse.