Improvements to the APBS biomolecular solvation software suite

Abstract

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK values, and an improved web-based visualization tool for viewing electrostatics.

Bxy‐fuca encoding α‐L‐fucosidase plays crucial roles in development and reproduction of the pathogenic pinewood nematode, Bursaphelenchus xylophilus

“… The Bxy‐FUCA homology model was produced using MODELLER 9.21 . The electrostatics potential was calculated by APBS (Adaptive Poisson‐Boltzmann Solver) . Autodock Vina was used to visual the interaction between fucose and Bxy‐FUCA.…”

Structural snapshots along the reaction mechanism of the atypical poplar thioredoxin‐like2.1

“…All structural figures were generated with pymol (v 1.8.1.0, Schrödinger, LLC, New York, NY, USA). Structure analyses were done using the program chimera (structure superimpositions) , the server http://www.rcsb.org/pdb/search/structidSearch.do?structureId=2PQR and the program apbs (electrostatic potential visualizations) , and the server EBI‐PISA (exploration of protein interfaces) .…”

A domain decomposition method for the polarizable continuum model based on the solvent excluded surface

“…First, one can obtain a generalized Poisson (GP) equation if ρ is independent on ψ as for the non-ionic solvent and second, a Poisson-Boltzmann equation [16] is obtained if the solvent contains ions whose movement is accounted for by Boltzmann statistics. Since the end of 1980s, many codes have been proposed for solving the Poisson-Boltzmann (or Poisson) equation for example using the boundary element method [7,35], the finite element method [2,24] or the finite difference method including UHBD [15], DelPhi [30], APBS [3,17,27] and the other work [18]. In particular, the APBS software is popular and widely used which can calculate the biomolecular electrostatics for large molecules.…”

“…We have obtained two PDEs of W and 26) and two boundary conditions coupling them 27) where σ is the density generating W ∞ by (4.21). To compute the electrostatic contribution to the solvation energy, we need to compute W which involves solving Eqs (4.26)-(4.27).…”