Work

MolPlay: Democratizing Interactive Molecular Simulations and Analyses with a Portable, Turnkey Platform

Year: 2024

Type: article

Abstract: Computer-based tools for visualizing and manipulating molecular structures in real-time hold immense potential for accelerating research and improving education, but are only used to a limited extent. This paper explores the possibilities of these powerful techniques and presents a classification of common interactive modeling tasks, such as assembly, deformation, sampling of rare events, along with relevant use cases, especially for the study of membranes and membrane proteins. I introduce MolPlay─a platform that provides a ready-to-use software environment with a curated set of hands-on examples to democratize access to interactive molecular simulations and analyses (IMSA). These research tools allow researchers to visualize, manipulate, and study digital models of molecules in real-time and can be started directly from a small, portable storage device. The portable, self-contained nature of MolPlay enables versatile deployment scenarios ranging from outreach to teaching in computer laboratories to facilitating the distribution of research software. Initial tests at an international workshop have shown that MolPlay appeals to different target groups and lowers the access barriers to IMSA. By consolidating more than a decade of expertise into one accessible platform, MolPlay represents a significant step toward broader adoption of these underutilized but powerful computational techniques in education and research.

Source: The Journal of Physical Chemistry B

DOI: 10.1021/acs.jpcb.4c04712

Author: Marc Baaden

Institutions: Centre National de la Recherche Scientifique, Université Paris Cité, Laboratoire de Biochimie Théorique

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funder: Agence Nationale de la Recherche

Awards: Interactive Pharmacophore using Augmented Reality, Data mining, Visualization and Computational Modeling of Redox Signaling Networks, Centre d'analyse de systèmes complexes dans les environnements complexes, Dynamique des membranes transductrices d'énergie : biogénèse et organisation supramoléculaire.