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

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.

Mass Analyzers: Common Types

Mass Analyzers: Common Types

The quadrupole mass analyzer consists of four cylindrical metal rods arranged in a diamond carrying a DC voltage and a radio-frequency AC voltage. The motion of ions through the quadrupole depends on the field strength, causing only ions of a certain m/z to resonate successfully and strike the detector at a given field strength. Though the transmission rate for these analyzers is high, the exact elemental composition of the sample is not determined because of low resolution; however, they are...

Molecular Shapes

Molecular Shapes

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...

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

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

Same author

Data augmentation in a triple transformer loop retrosynthesis model.

Digital discovery·2026

Search research articles

Related Experiment Video

Updated: May 6, 2026

Construction of a High Resolution Microscope with Conventional and Holographic Optical Trapping Capabilities

Construction of a High Resolution Microscope with Conventional and Holographic Optical Trapping Capabilities

Published on: April 22, 2013

Nested TMAPs to Visualize Billions of Molecules.

Alejandro Flores Sepúlveda¹, Jean-Louis Reymond¹

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

Journal of Chemical Information and Modeling

|May 4, 2026

Summary

This summary is machine-generated.

This study introduces a novel framework for exploring massive chemical datasets, like the REAL database of 9.6 billion molecules. It enables efficient visualization and clustering of molecular structures using molecular quantum numbers (MQN) and tree-maps (TMAP).

More Related Videos

Neutrophil Extracellular Traps: How to Generate and Visualize Them

Neutrophil Extracellular Traps: How to Generate and Visualize Them

Published on: February 24, 2010

Experimental Methods for Trapping Ions Using Microfabricated Surface Ion Traps

Experimental Methods for Trapping Ions Using Microfabricated Surface Ion Traps

Published on: August 17, 2017

Related Experiment Videos

Last Updated: May 6, 2026

Construction of a High Resolution Microscope with Conventional and Holographic Optical Trapping Capabilities

Construction of a High Resolution Microscope with Conventional and Holographic Optical Trapping Capabilities

Published on: April 22, 2013

Neutrophil Extracellular Traps: How to Generate and Visualize Them

Neutrophil Extracellular Traps: How to Generate and Visualize Them

Published on: February 24, 2010

Experimental Methods for Trapping Ions Using Microfabricated Surface Ion Traps

Experimental Methods for Trapping Ions Using Microfabricated Surface Ion Traps

Published on: August 17, 2017

Area of Science:

Cheminformatics
Computational Chemistry
Data Visualization

Background:

Exploring large chemical datasets is computationally challenging.
Efficient methods are needed to navigate and understand molecular diversity.

Purpose of the Study:

To develop a visualization and clustering framework for billion-sized chemical data sets.
To enable efficient exploration of the REAL database of 9.6 billion molecules.

Main Methods:

Molecules represented by 42-dimensional molecular quantum numbers (MQN) fingerprints.
Clustering performed using Product Quantization and PQk-Means.
Tree-map (TMAP) visualization linking representatives and substructure similarity.

Main Results:

A framework for exploring billion-sized chemical data sets was successfully developed.
Nested TMAPs provide direct access to molecular structures within clusters.
The REAL database exploration is accessible via a web link.

Conclusions:

The presented framework offers an efficient method for exploring massive chemical datasets.
Nested TMAPs facilitate rapid navigation from cluster representatives to individual molecules.
This approach is computationally feasible on a single workstation.