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

Rab Proteins01:14

Rab Proteins

4.9K
Rab proteins constitute the largest family of monomeric GTPases, of which 70 members are present in humans. Rab proteins and their effectors regulate consecutive stages of vesicle transport such as vesicle transport, docking, and fusion to the correct recipient membrane.
Rab proteins switch between a cytosolic, GDP-bound inactive state and a membrane-anchored, GTP-bound active state. By themselves, Rabs show slow rates of GDP/GTP exchange and GTP hydrolysis. Thus, Rab proteins are considered...
4.9K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

5.0K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
5.0K
Rab Cascades01:25

Rab Cascades

3.4K
Rab GTPases act in a regulated cascade during membrane fusion, helping the lipid bilayers mix. The Rab family of proteins are active when bound to GTP, and inactive when bound to GDP. Hence, they act as guanine nucleotide-dependent molecular switches. Rab-GTP recognizes and binds to long or short-range tethering proteins to capture the target vesicle. These tethers coordinate with SNAREs on the vesicle and the target membrane to assemble the trans SNARE complex that locks the mixing bilayers.
3.4K
Ribosome Profiling02:24

Ribosome Profiling

4.1K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.1K
Protein Modifications in the RER01:26

Protein Modifications in the RER

6.9K
Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal...
6.9K
Gene Families01:57

Gene Families

9.8K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
9.8K

You might also read

Related Articles

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

Sort by
Same author

Living bacterial reservoir computers for information processing and sensing.

Cell systems·2026
Same author

Active-learning-guided optimization of cell-free systems for genome-wide transcriptomic profiling reveals progressive layers of regulation.

Nature communications·2026
Same author

dAMN: a genome-scale neural-mechanistic hybrid model to predict bacterial growth dynamics.

Bioinformatics (Oxford, England)·2026
Same author

RetroRules 2026: an expanded database combining biochemical and organic reaction templates for pathway discovery.

Nucleic acids research·2025
Same author

Microbial computing: Review and Perspectives.

Biotechnology advances·2025
Same author

An AI-driven workflow for the accelerated optimization of cell-free protein synthesis.

iScience·2025
Same journal

SowPostureDS: A Multi-Class Image Dataset for YOLO-Based Detection of Sow Postures in diverse Farrowing Systems.

Scientific data·2026
Same journal

A Pulmonary Ultrasound Dataset for Tumor Segmentation and Classification.

Scientific data·2026
Same journal

An open dataset of cerebral tau deposition in young healthy adults based on [<sup>18</sup>F]MK6240 positron emission tomography.

Scientific data·2026
Same journal

GLORIF1, a global river flow dataset created by integrating process-based modelling and machine learning.

Scientific data·2026
Same journal

Curated endoscopic retrograde cholangiopancreatography images dataset.

Scientific data·2026
Same journal

Age-Specific Cerebral Vessel Templates Across the Lifespan of Healthy Adults.

Scientific data·2026
See all related articles

Related Experiment Video

Updated: Jan 14, 2026

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion
07:37

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

Published on: June 25, 2017

12.1K

BioRGroup dataset: R-group expansion of ChEBI molecules referenced in the Rhea database.

Guillaume Gricourt1, Jean-Loup Faulon2,3

  • 1Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France. guillaume.gricourt@inrae.fr.

Scientific Data
|October 28, 2025
PubMed
Summary
This summary is machine-generated.

Artificial intelligence in cheminformatics requires complete chemical data. A new dataset, BioRGroup, resolves generic R-group structures from ChEBI into specific molecules for enhanced computational analysis.

More Related Videos

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
10:43

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

11.6K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.4K

Related Experiment Videos

Last Updated: Jan 14, 2026

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion
07:37

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

Published on: June 25, 2017

12.1K
Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
10:43

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

11.6K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.4K

Area of Science:

  • Cheminformatics
  • Computational Chemistry
  • Biocatalysis

Background:

  • Artificial intelligence (AI) in cheminformatics necessitates comprehensive chemical datasets.
  • Specialized databases like Rhea (using ChEBI ontology) are vital for enzyme-catalyzed reactions but contain generic R-group structures.
  • These generic structures hinder computational applications like retro-biosynthesis and biocatalysis.

Purpose of the Study:

  • To address the challenge of generic R-group structures in chemical databases.
  • To create a curated dataset resolving R-group containing entries into fully defined molecular instances.
  • To enhance the utility of under-utilized chemical information in computational workflows.

Main Methods:

  • Extraction of generic molecules from the Rhea database.
  • Identification of compatible substitutions using PubChem and RDKit.
  • Application of tailored filters for generating chemically valid molecular enumerations.
  • Creation of the BioRGroup dataset in a standard file format.

Main Results:

  • A novel curated dataset, BioRGroup, was generated.
  • R-group-containing ChEBI entries were resolved into specific molecular instances.
  • The dataset enables the integration of previously under-utilized generic chemical structures.

Conclusions:

  • The BioRGroup dataset enhances the scope and granularity of chemical data analysis.
  • It facilitates the use of specialized chemical reaction data in AI-driven cheminformatics.
  • This work improves computational pipelines for retro-biosynthesis and biocatalysis.