Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1.0]

Abstract

Electrostatics play indispensable role in practically any process in molecular biology. Indeed, at distances larger than several Angstroms all other forces are negligibly small and electrostatic force dominates. However, modeling electrostatics in molecular biology is a complicated task due to presence of water phase, mobile ions and irregularly shaped inhomogeneous biological macromolecules. A particular approach to calculating electrostatics in such systems is to apply Poisson-Boltzmann equation (PBE). Here we provide a tutorial for the popular DelPhi package that solves PBE using a finite difference method and returns the electrostatic potential distribution throughout the modeling box. The tutorial comes with detailed description of different tasks that DelPhi can handle, an assessment of the accuracy against cases with analytical solution and recommendations about DelPhi usage. Furthermore, since electrostatics is a key component of virtually any modeling in molecular biology, we have created many additional resources utilizing DelPhi to model various biology relevant quantities. Tutorials for these resources are also provided along with examples of their usage.