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Related Experiment Video

Updated: Jul 15, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Surfaces: a software to quantify and visualize interactions within and between proteins and ligands.

Natália Teruel¹, Vinicius Magalhães Borges², Rafael Najmanovich¹

¹Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal H3T 1J4, Canada.

Bioinformatics (Oxford, England)

|October 3, 2023

Summary

We developed Surfaces, a fast software tool to quantify molecular interactions and their impact on biomolecular stability. This method correlates well with experimental data, offering a computationally efficient alternative to complex simulations.

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Area of Science:

Computational biology
Structural biology
Biophysics

Background:

Understanding molecular interactions is crucial for analyzing biomolecular stability and engineering biological processes.
Existing computational methods can be computationally expensive and complex to use.

Purpose of the Study:

To present Surfaces, a novel software for quantifying and visualizing molecular interactions.
To provide an easy-to-use, fast, and customizable tool for assessing the contribution of molecular interactions to biomolecular stability.

Main Methods:

The Surfaces software calculates the contact surface areas between molecules.
This approach quantifies the relative contribution of molecular interactions to stability.

Main Results:

Surfaces provides accurate quantification and visualization of molecular interactions.
The software's performance shows correlations with experimental data comparable or superior to computationally intensive methods like molecular dynamics.

Conclusions:

Surfaces offers an efficient and effective computational approach for studying biomolecular interactions and stability.
The software is accessible and customizable for researchers in computational and structural biology.