The Representation of Electrostatics for Biological Molecules

Abstract

Biological molecules live in an environment in which most of the forces that determine their activity are (at least apparently) different from those that guide the world visible to humans. These forces can be roughly classified as Brownian motion, lipophilic/hydrophilic interactions, and electrostatic potential. In the study and representation of proteins and other biological molecules, and especially their activity and interaction, it is therefore extremely important to be able to observe these forces in a meaningful way. This will lead to better understanding of dynamic interactions, and for a greater capacity for description and manipulation. While the calculation of these forces typically provides numerical data, it is not always easy and intuitive to have them represented in a way that makes sense to human beings, whose visual intelligence is one of the most highly developed. In the past few years, we have developed BioBlender, a software program dedicated to the intuitive visualization of proteins, their properties, and their interactions with other proteins, other biological molecules, and the cellular environment. BioBlender is based on Blender, one of the most powerful engines of Computer Graphics (CG) for 3D content management, i.e., creation, animation, texturing, and rendering of visual objects and scenes. Blender is the only complete program dedicated to 3D that is open source, a feature important for users who want or need to introduce new features, in our case the ability to handle biological objects starting from files in PDB format. In this chapter, we will consider some issues of molecular visualization, and describe some of the features of BioBlender, with particular focus on the calculation and rendering of Electrostatic Potential (EP).