Background

The application domain of the PyGBe code (pronounced’pig-bee’) is electrostatics in biology. At a microscopic level, electrostatic effects control a majority of biological processes, 2 for example, the affinity of 2 A. Warshel, PK Sharma, M. Kato, and WW Parson. Modeling electrostatic effects in proteins. Biochim. Biophys. Acta, 1764: 1647–1676, 2006 two biological compounds to bind or the catalytic power of enzymes. Calculating electrostatic energies is an effective way to study protein systems, often being capable of providing quantitative predictions. In biology, proteins are never isolated; they are dissolved in water with salts and other proteins. Hence, the interactions between charges in a biological system are screened by the presence of water with dissolved ions. In this case, the classical treatment of electrostatics effects uses the Debye-Hückel approximation, where charges obey a Boltzmann distribution. Combined with the Poisson equation for the potential field, we obtain the Poisson-Boltzmann equation, which is the starting point of our model.

The model for biomolecular electrostatics based on the Poisson-Boltzmann equation is a semi-macroscopic approach: the region occupied by water (with dissolved ions) is represented by a continuum dielectric, and the region occupied by the protein is represented by a low-dielectric material with embedded point charges at the atom locations. It is referred to as an implicit solvent model.