Electrostatics play an 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 the Poisson-Boltzmann equation (PBE). Here, we provide a tutorial for the popular DelPhi package that solves PBE using a finite-difference method and delivers the electrostatic potential distribution throughout the modeling box. The tutorial comes with a detailed description of different tasks that DelPhi can handle, an assessment of the accuracy against cases with analytical solutions 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.

Abstract Background: Ions play significant roles in biological processes - they may specifically bind to a protein site or bind non-specifically on its surface. Though, the role of specifically bound ions range from actively providing structural compactness via coordination of charge-charge interactions to numerous enzymatic activities, non-specifically surface-bound ions are also crucial to maintaining a protein’s stability, responding to pH and ion concentration changes and contributing to other biological processes. However, experimental determination of positions of non-specifically bound ions is not trivial since they may have low residential time and experience significant thermal fluctuation of their positions. Results: Here we report a new release of a computational method, the BION-2 method, that predicts positions of non-specifically surface-bound ions. The BION-2 utilizes the Gaussian-based treatment of ions within the framework of the modified Poisson-Boltzmann equation, that does not require a sharp boundary between the protein and water phase. Thus, the predictions are done by the balance of the energy of interaction between the protein charges and the corresponding ions, and the de-solvation penalty of the ions as they approach the protein. Conclusions: The BION-2 is tested against experimentally determined ion’s positions, with both X-ray and NMR determined positions, and it is demonstrated that it outperforms the old BION and molecular dynamics tools. The BION-2 is available as a web server as well.

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