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Modeling an Enzyme Active Site using Molecular Visualization Freeware
Published on: December 25, 2021
The MolecularWeb Universe: Web-Based, Immersive, Multiuser Molecular Graphics and Modeling
Fabio J Cortés Rodríguez1, Lucien F Krapp1, Fernando Teixeira Pinto Meireles1
1Laboratory for Biomolecular Modeling and Protein Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
Methods in Molecular Biology (Clifton, N.J.)
|July 9, 2026
Summary
eXtended Reality (XR) tools like MolecularWeb and HandMol are revolutionizing molecular visualization and modeling. These web-based platforms offer accessible, interactive 3D experiences for education, science communication, and research, enhancing how we interact with molecular structures.
Area of Science:
- Chemical and structural sciences
- Computational chemistry
- Scientific visualization
Background:
- Traditional 2D interfaces limit the understanding and manipulation of 3D molecular structures.
- eXtended Reality (XR) technologies, including augmented reality (AR) and virtual reality (VR), offer immersive solutions for molecular sciences.
- Accessibility to advanced molecular visualization tools remains a challenge for many researchers and educators.
Purpose of the Study:
- To introduce the MolecularWeb ecosystem, a suite of web-based tools for accessible immersive molecular visualization and interactive modeling.
- To showcase the development and applications of MolecularWeb, MolecularWebXR, PDB2AR, and HandMol prototypes.
- To demonstrate how XR technologies can enhance molecular science education, communication, and research.
Main Methods:
- Development of web-based AR and VR platforms (MolecularWeb, MolecularWebXR) accessible via various devices.
- Creation of tools for generating custom AR/VR content (PDB2AR).
- Prototyping of immersive 3D molecular modeling with natural language interaction and real-time calculations (HandMol).
Main Results:
- MolecularWeb provides AR activities for education on standard devices.
- MolecularWebXR enables multiuser immersive experiences for chemistry, materials science, and structural biology outreach and discussion.
- HandMol prototypes offer intuitive, hands-on 3D molecular modeling with advanced features like AI interpretation and on-the-fly calculations.
Conclusions:
- The MolecularWeb ecosystem significantly enhances accessibility to immersive molecular visualization and modeling.
- XR technologies integrated into web platforms are transforming molecular science education and research.
- Future molecular science interactions will be more intuitive, collaborative, and accessible through these advanced web-based XR tools.
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