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

39.3K
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.
39.3K
Nucleic Acid Structure01:25

Nucleic Acid Structure

6.3K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
6.3K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

44.0K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
44.0K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

77
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
77
DNA Microarrays02:34

DNA Microarrays

18.1K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
18.1K

You might also read

Related Articles

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

Sort by
Same author

Mechanistic basis of teichoic acid transport by a gatekeeper flippase.

Nature communications·2026
Same author

Nested TMAPs to Visualize Billions of Molecules.

Journal of chemical information and modeling·2026
Same author

Correction to "Exploring Simple Drug Scaffolds from the GDB Chemical Space Reveals a Chiral Bicyclic Azepane with Potent Neuropharmacology".

Journal of medicinal chemistry·2026
Same author

Structures of ALG3/9/12 reveal the assembly logic of the N-glycan oligomannose core.

Nature chemical biology·2026
Same author

Mechanistic basis of teichoic acid transport by a gatekeeper flippase.

bioRxiv : the preprint server for biology·2026
Same author

Polypharmacology Browser PPB3: A Web-Based Deep Learning Tool for Target Prediction Using ChEMBL Data.

Journal of chemical information and modeling·2026

Related Experiment Video

Updated: Aug 16, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.7K

Molecular Framework Analysis of the Generated Database GDB-13s.

Ye Buehler1, Jean-Louis Reymond1

  • 1Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012Bern, Switzerland.

Journal of Chemical Information and Modeling
|December 19, 2022
PubMed
Summary

Generated chemical databases (GDBs) contain novel molecular frameworks (MFs) distinct from public databases. These unique and simple MFs offer promising avenues for innovative synthetic chemistry.

More Related Videos

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.5K
Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules
07:11

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

6.9K

Related Experiment Videos

Last Updated: Aug 16, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.7K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.5K
Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules
07:11

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

6.9K

Area of Science:

  • Computational Chemistry
  • Medicinal Chemistry
  • Drug Discovery

Background:

  • Generated databases (GDBs) systematically enumerate billions of chemically plausible molecules.
  • Assessing molecular originality is crucial for identifying novel chemical entities.

Purpose of the Study:

  • To evaluate the novelty of molecules within GDBs by comparing their molecular frameworks (MFs) against existing public databases.
  • To identify unique MFs in GDBs that could serve as starting points for innovative molecular design.

Main Methods:

  • Utilized Bemis-Murcko molecular frameworks (MFs) as a method for comparing molecular structures.
  • Compared GDB-13s MFs against MFs from large public databases: ZINC, PubChem50, and COCONUT.
  • Analyzed MF characteristics, including ring sizes, ring systems, and the presence of linker bonds.

Main Results:

  • GDB-13s MFs exhibited greater diversity in ring sizes and ring systems compared to public databases.
  • A significant portion of GDB-13s MFs were not found in ZINC, PubChem50, or COCONUT, indicating high exclusivity.
  • GDB-13s MFs often lacked linker bonds, unlike those prevalent in public databases.

Conclusions:

  • GDBs represent a rich source of novel molecular frameworks with high originality.
  • The unique and relatively simple MFs in GDBs are attractive targets for synthetic chemists seeking to create innovative molecules.
  • This study highlights the potential of GDBs for advancing drug discovery and chemical innovation.