APBS: Nanoscale Biomolecular Electrostatics Software

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Project description The goal of this project is to enable the investigation of macromolecular solvation and electrostatic properties in biomedical research by supporting the maintenance and continued development of the open- source Adaptive Poisson-Boltzmann Solver (APBS) and PDB2PQR software packages. An understanding of electrostatic interactions is essential for the study of biomolecular processes. The structures of proteins and other biopolymers are being determined at an increasing rate through structural genomics and other efforts, while specific linkages of these biopolymers in cellular pathways or supramolecular assemblages are being detected by genetic and proteomic studies. To integrate this information in physical models for drug discovery or other applications requires the ability to evaluate the energetic interactions within and between biopolymers. Among the various components of molecular energetics, solvation properties and electrostatic interactions are of special importance because of the long range of these interactions and the substantial charges of typical biopolymer components. APBS is a unique software package that solves the equations of continuum electrostatics for large biomolecular assemblages. This software has been designed “from the ground up” using modern design principles to ensure its ability to interface with other computational packages and evolve as methods and applications change over time. The APBS code is accompanied by extensive documentation for both users and programmers and is supported by a variety of utilities for preparing calculations and analyzing results. Finally, the free, open-source APBS license ensures its accessibility to the entire biomedical community. The use of continuum solvation methods such as APBS requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. PDB2PQR provides a software solution for repairing/completing structures, performing such parameterization, assigning biomolecular titration states, and visualizing the results – capabilities designed for researchers with a wide range of expertise.