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Updated: Jul 9, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware
Published on: December 25, 2021
Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using
Fabio Cortés Rodriguez1, Lucien F Krapp2, Matteo Dal Peraro3
1Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland. fabio.cortesrodriguez@epfl.ch.
Abstract:
moleculARweb (https://molecularweb.epfl.ch) began as a website for education and outreach in chemistry and structural biology through augmented reality (AR) content that runs in the web browsers of regular devices like smartphones, tablets, and computers. Here we present two evolutions of moleculARweb's Virtual Modeling Kits (VMK), tools where users can build and view molecules, and explore their mechanics, in 3D AR by handling the molecules in full 3D with custom-printed cube markers (VMK 2.0) or by moving around a simulated scene with mouse or touch gestures (VMK 3.0). Upon simulation the molecules experience visually realistic torsions, clashes, and hydrogen-bonding interactions that the user can manually switch on and off to explore their effects. Moreover, by manually tuning a fictitious temperature the users can accelerate conformational transitions or 'freeze' specific conformations for careful inspection in 3D. Even some phase transitions and separations can be simulated. We here showcase these and other features of the new VMKs connecting them to possible specific applications to teaching and self-learning of concepts from general, organic, biological and physical chemistry; and in assisting with small tasks in molecular modelling for research. Last, in a short discussion section we overview what future developments are needed for the 'dream tool' for the future of chemistry education and work.
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