Intuitive representation of surface properties of biomolecules using BioBlender

TL;DR

BioBlender is an open-source tool that uses Blender to intuitively visualize surface properties like electrostatic potential and hydropathy of biomolecules, enhancing understanding of their physical and chemical features through animation.

Contribution

It introduces a novel visualization approach for biomolecular surface properties using open-source 3D animation software, integrating physico-chemical calculations with visual representation.

Findings

Visualizes electrostatic potential as flowing particles along field lines.

Depicts hydropathy with photorealistic surface coloring.

Enables continuous visualization during protein motion.

Abstract

In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the visualization (here) of proteins and other macromolecules, using instruments of computer graphics. The availability of protein structures enables the study of their surfaces and surface properties such as electrostatic potential (EP) and hydropathy (MLP), based on atomic contribution. Recent advances in 3D animation and rendering software have not yet been exploited for the representation of proteins and other biological molecules in an intuitive, animated form. Taking advantage of an open-source, 3D animation and rendering software, Blender, we developed BioBlender, a package dedicated to biological work: elaboration of proteins' motions with the simultaneous visualization of chemical and physical features. EP and MLP are calculated using physico-chemical programs and custom programs and scripts, organized and accessed within BioBlender interface. A new visual code is introduced for MLP visualization: a range of optical features that permits a photorealistic rendering of its spatial distribution on the surface of the protein. EP is represented as animated line particles that flow along field lines proportional to the total charge of the protein. Our system permits EP and MLP visualization of molecules and, in the case of moving proteins, the continuous perception of these features, calculated for each intermediate conformation. Using real world tactile/sight feelings, the nanoscale world of proteins becomes more understandable, familiar to our everyday life, making it easier to introduce "un-seen" phenomena (concepts) such as hydropathy or charges.