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

Plotting of Topographic Maps

Plotting of Topographic Maps

Topographic maps represent the Earth's surface features using contour lines, which connect points of equal elevation to create a two-dimensional representation of three-dimensional terrain. Creating a topographic map requires a systematic approach.Begin by plotting a scaled grid and marking intersections corresponding to the survey's elevation data points. Assign elevation values at these intersections to build the base map. Next, determine contour levels using a consistent contour interval,...

Newman Projections

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...

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

Search for Light Pseudoscalar Bosons, Pair-Produced in Higgs Boson Decays in the Four-Electron Final State in Proton-Proton Collisions at sqrt[s]=13 TeV.

Physical review letters·2026

Same author

First Evidence for Mixing-Induced CP Violation in B_{s}^{0}→J/ψϕ(1020) Decays in pp Collisions at sqrt[s]=13 TeV.

Physical review letters·2026

Same author

Observation of Suppressed Charged-Particle Production in Ultrarelativistic Oxygen-Oxygen Collisions.

Physical review letters·2026

Same author

Measurement of D^{0} Meson Photoproduction in Ultraperipheral Heavy Ion Collisions.

Physical review letters·2026

Same author

Observation of tWZ Production at the CMS Experiment.

Physical review letters·2026

Same author

First Exclusive Reconstruction of the B^{+}, B^{0}, and B_{s}^{*0} Mesons and Precise Measurement of Their Masses.

Physical review letters·2026

Same journal

SpaceExpander: An Automated System for Drafting Markush Claims to Expand Chemical Space.

Molecular informatics·2026

Same journal

A Structure-Informed Atlas of Venom-Derived Peptides Reveals the Organization of Chemical Space.

Molecular informatics·2026

Same journal

ConGen: Targeted Molecule Generation Through Contrastive Learning and Latent Optimization.

Molecular informatics·2026

Same journal

Novel Molecules Generation Using Graph Generative Adversarial Networks.

Molecular informatics·2026

Same journal

An Attention-Driven Graph Transformer With Nonlinear Modeling and Neuro-Fuzzy Fusion for High-Order Toxic Molecular Graph Learning.

Molecular informatics·2026

Same journal

Molecular Modeling and Chemoinformatics in Ukraine.

Molecular informatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Feb 23, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Neighboring Structure Visualization on a Grid-based Layout.

G Marcou¹, D Horvath¹, A Varnek¹

¹Laboratory of Chemoinformatics, University of Strasbourg, 1 rue Biaise Pascal, 67000, Strasbourg, France.

Molecular Informatics

|September 14, 2017

Summary

This summary is machine-generated.

This study introduces a new algorithm for visualizing chemical structures, arranging similar molecules near each other on various layouts. The method uses the Hilbert Schmidt Independence Criterion for effective structure reordering and visualization.

Keywords:

Dopamine D5 Visualization kernel method optimal assignment sorting

More Related Videos

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

Published on: September 28, 2019

Automated Charting of the Visual Space of Housefly Compound Eyes

Automated Charting of the Visual Space of Housefly Compound Eyes

Published on: March 31, 2022

Related Experiment Videos

Last Updated: Feb 23, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

Published on: September 28, 2019

Automated Charting of the Visual Space of Housefly Compound Eyes

Automated Charting of the Visual Space of Housefly Compound Eyes

Published on: March 31, 2022

Area of Science:

Computational chemistry
Cheminformatics
Data visualization

Background:

Visualizing chemical structures is crucial for understanding molecular relationships.
Existing methods may not effectively group similar structures in a spatial layout.
Developing novel algorithms can enhance molecular data analysis.

Purpose of the Study:

To present a new algorithm for visualizing chemical structures.
To ensure that similar chemical structures are positioned adjacently in a grid-based layout.
To demonstrate the algorithm's applicability across different layout types.

Main Methods:

Developed an algorithm for chemical structure visualization.
Employed structure reordering based on the Hilbert Schmidt Independence Criterion.
Applied the method to bi- or three-dimensional shapes.

Main Results:

Successfully visualized a set of dopamine D5 ligands.
Demonstrated the algorithm's effectiveness on squared, disk, and spherical layouts.
Achieved neighboring placement of similar chemical structures.

Conclusions:

The proposed algorithm provides an effective method for visualizing chemical structures.
The Hilbert Schmidt Independence Criterion aids in achieving similarity-based spatial organization.
The approach is versatile and applicable to diverse layout geometries.