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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.

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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.

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Related Experiment Video

Updated: Jun 13, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Mesoscale Explorer - Visual Exploration of Large-Scale Molecular Models.

Alexander Rose¹, David Sehnal², David S Goodsell^3,4

¹independent.

Biorxiv : the Preprint Server for Biology

|September 16, 2024

Summary

This summary is machine-generated.

Mesoscale Explorer enables interactive web-based visualization of large molecular models, like viruses and organelles, using cryo-electron microscopy data. This tool enhances understanding of complex biological structures.

Keywords:

3D animation interactive tours mesoscale models molecular graphism web-based 3D visualization

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Last Updated: Jun 13, 2025

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Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) generate large-scale 3D models of biological macromolecules.
Visualizing these complex models, comprising billions of atoms, traditionally requires specialized software and hardware.
Advancements in GPU rendering and web technologies now permit interactive visualization directly in web browsers.

Purpose of the Study:

To introduce Mesoscale Explorer, a novel web application for visualizing large molecular models.
To leverage the Mol* framework for efficient rendering of complex biological structures.
To provide accessible and insightful exploration of macromolecular assemblies.

Main Methods:

Development of a web application, Mesoscale Explorer.
Utilization of the Mol* JavaScript framework for molecular visualization.
Integration of GPU rendering capabilities for interactive display.

Main Results:

Mesoscale Explorer successfully renders large-scale molecular models, including viruses and cellular organelles, interactively.
The application facilitates enhanced perception and streamlined exploration of complex biological data.
Diverse data types can be visualized with clarity, revealing intricate structural details.

Conclusions:

Mesoscale Explorer democratizes access to large molecular model visualization.
The tool enhances scientific understanding by simplifying the exploration of complex biological structures.
Web-based visualization of macromolecular assemblies is now feasible and effective.