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Molecular Models

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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.

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Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...

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Related Experiment Video

Updated: May 24, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

CheS-Mapper - Chemical Space Mapping and Visualization in 3D.

Martin Gütlein¹, Andreas Karwath, Stefan Kramer

¹Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany. guetlein@informatik.uni-freiburg.de.

Journal of Cheminformatics

|March 20, 2012

Summary

This summary is machine-generated.

CheS-Mapper is a new 3D molecular viewer that helps chemoinformatics researchers visualize chemical datasets. It clusters similar compounds in 3D space, aiding in understanding structure-activity relationships and identifying patterns.

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy

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Last Updated: May 24, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Area of Science:

Chemoinformatics
Computational Chemistry
Data Visualization

Background:

Analyzing complex chemical datasets is challenging for researchers.
Understanding relationships between chemical structure, properties, and biological effects is difficult.
Visualization tools can aid in comprehending correlations within chemical data.

Purpose of the Study:

To introduce CheS-Mapper, a novel 3D molecular viewer for chemical datasets.
To facilitate the understanding of structure-activity relationships through data visualization.
To enable interactive exploration and analysis of chemical compound similarity.

Main Methods:

Development of a 3D molecular viewer, CheS-Mapper (Chemical Space Mapper).
Implementation of clustering algorithms to group similar chemical compounds.
Utilizing user-selectable features, including structural fragments and chemical descriptors, for similarity assessment.
3D spatial arrangement where proximity indicates similarity.

Main Results:

CheS-Mapper effectively clusters large chemical datasets based on user-defined features.
The 3D visualization aids in identifying patterns and regularities within the data.
Users can interactively explore and highlight specific chemical features.
The tool supports the selection and export of specific data subsets for further analysis.

Conclusions:

CheS-Mapper provides an effective solution for visualizing and analyzing complex chemical datasets.
The tool enhances the understanding of chemical space and structure-activity relationships.
CheS-Mapper empowers chemists to explore, interpret, and select data for further research.