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A VR app which allows creation and manipulation of dynamic models of polypeptides. Focus is fun and learning.
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README.md

README.md

“Peppy” Interactive Peptide

Latest versions:

Oculus Rift/PC https://github.com/ddoak/peppy/releases/tag/v0.64b

Oculus Quest https://github.com/ddoak/peppy/releases/tag/v0.63-q

A virtual reality application which allows the user to create and directly manipulate dynamic models of polypeptide molecules in real time.

Goals:

visualisation / teaching / molecular modelling 'sketching'

encourage experiential learning about polypeptide properties and conformation through play

Features:

a responsive interactive polypeptide backbone built from simple primitives

Unity physics joints used to represent bonded / non-bonded interactions (e.g. dihedrals / hydrogen bonds)

basic electrostatics

simple dynamics

sidechain mutation

not intended to be a simulation

Who is it for?

The intended users are tertiary level students studying protein structure but it is hoped that it will have wider appeal to a popular science audience.

Why is it needed?

The goal is to create an intuitive, flexible and fun modern learning tool which encourages users to interactively explore the principles underpinning protein structure and molecular dynamics. Kinaesthetic learning through experiential play is a highly effective way to build a deep foundational understanding of this subject and to pique users’ curiosity to inquire further elsewhere.

How does it work?

The app allows the user to ‘spawn’ polypeptide chains which can then be ‘physically’ grabbed and manipulated in the virtual space – through pushing, pulling, twisting and ‘touching’ these molecules higher order structures can be created or destroyed and their stability and properties investigated. The minimal sandbox game-like environment encourages playful self-directed creative engagement. Interaction is immediate and intuitive and is built on both the immersive nature of VR and the revolutionary interface possibilities afforded by fully tracked (6DOF) motion controllers. Many of the low level simulation parameters (e.g. force constants, dynamics) are exposed to the user and can be manipulated directly at runtime and the consequential effects observed. This is not intended to be a robust and detailed molecular dynamics simulation – however it is highly effective as a representative sketch which allows the user to experiment and explore many of the emergent structural properties of proteins such as repeating secondary elements. Hydrogen bonds and electrostatic interactions are modelled in a simplified manner and are represented graphically by animated particle effects which visualise the dynamic forces involved.

Backbone (phi and psi) dihedrals are visualised on an interactive ‘Ramachandran’ plot and can be manipulated and monitored by the user. Primary sequence can be easily altered and sidechain conformations and steric properties investigated. An in-game camera allows the user to record snapshots of their creations. It is also possible to run the application in a ‘flat’ nonVR mode – this presents the same innovative dynamic functionality but is limited by a more traditional mouse/keyboard interface.

Why is it good?

It is hoped that the app is fun to engage with and presents the basic elements of protein structure in an accessible format which is novel, dynamic and extremely tangible. It is possible to easily and quickly investigate a wide range of conformational properties of the polypeptide backbone and sidechains. The intention is that the experience and insights offered are progressive and complement what has previously been generally available (i.e. from print, physical models, 3D graphics). The simplicity of the simulation becomes a strength when framed within the teaching and learning process. The physical parameters and assumptions of the underlying model are accessible and transparent - indeed, many of them can be altered at runtime. This invites active challenge, questioning and critique by the students. Investigating the limits of the model is an important step toward a deeper understanding of the subject.

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