Pepblock Builder VR – an Open-Source Tool for Gaming-Based Bio-Edutainment in Interactive Protein Design

Authors

Venkata V. B. Yallapragada, Cancer Research @ UCC, University College Cork, Cork, Ireland; SynBioCentre, University College Cork, Cork, IrelandFollow
Tianshu Xu, School of Computer Science and Information Technology, University College Cork, Cork, Ireland
Sidney P. Walker, Cancer Research @ UCC, University College Cork, Cork, Ireland; SynBioCentre, University College Cork, Cork, Ireland
Sabin Tabirca, School of Computer Science and Information Technology, University College Cork, Cork, Ireland; Department of Computer Science, Transylvania University of Brasov, Brasov, Romania
Mark Tangney, Cancer Research @ UCC, University College Cork, Cork, Ireland; SynBioCentre, University College Cork, Cork, Ireland; School of Computer Science and Information Technology, University College Cork, Cork, Ireland; Department of Computer Science, Transylvania University of Brasov, Brasov, Romania

ORCID

https://orcid.org/0000-0002-1766-0617

Document Type

Article

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Disciplines

Biomedical | Biotechnology | Electrical and Computer Engineering | Electromagnetics and Photonics | Engineering

Publication Details

Frontiers in Bioengineering and Biotechnology, vol. p, no. 674211. © 2021 Yallapragada, Xu, Walker, Tabirca and Tangney.

Abstract

Proteins mediate and perform various fundamental functions of life. This versatility of protein function is an attribute of its 3D structure. In recent years, our understanding of protein 3D structure has been complemented with advances in computational and mathematical tools for protein modelling and protein design. 3D molecular visualisation is an essential part in every protein design and protein modelling workflow. Over the years, stand-alone and web-based molecular visualisation tools have been used to emulate three-dimensional view on computers. The advent of virtual reality provided the scope for immersive control of molecular visualisation. While these technologies have significantly improved our insights into protein modelling, designing new proteins with a defined function remains a complicated process. Current tools to design proteins lack user-interactivity and demand high computational skills. In this work, we present the Pepblock Builder VR, a gaming-based molecular visualisation tool for bio-edutainment and understanding protein design. Simulating the concepts of protein design and incorporating gaming principles into molecular visualisation promotes effective gamebased learning. Unlike traditional sequence-based protein design and fragment-based stitching, the Pepblock Builder VR provides a building block style environment for complex structure building. This provides users a unique visual structure building experience. Furthermore, the inclusion of virtual reality to the Pepblock Builder VR brings immersive learning and provides users with “being there” experience in protein visualisation. The Pepblock Builder VR works both as a stand-alone and VR-based application, and with a gamified user interface, the Pepblock Builder VR aims to expand the horizons of scientific data generation to the masses.

Recommended Citation

Yallapragada VVB, Xu T, Walker SP, Tabirca S and Tangney M (2021) Pepblock Builder VR – An Open-Source Tool for Gaming-Based Bio-Edutainment in Interactive Protein Design. Front. Bioeng. Biotechnol. 9:674211. doi: 10.3389/fbioe.2021.674211