PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

Abstract

Continuum solvation models, such as Poisson-Boltzmann and Generalized Born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. However, the use of such methods requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing atomic coordinates to molecular structures from the Protein Data Bank and the assignment of parameters to biomolecular structures. To address this problem, we have developed the PDB2PQR web service (http://agave.wustl.edu/pdb2pqr/). This server automates many of the common tasks of preparing structures for continuum electrostatics calculations, including adding a limited number of missing heavy atoms to biomolecular structures, estimating titration states and protonating biomolecules in a manner consistent with favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields, and finally generating 'PQR' output compatible with several popular computational biology packages. This service is intended to facilitate the setup and execution of electrostatics calculations for both experts and non-experts and thereby broaden the accessibility to the biological community of continuum electrostatics analyses of biomolecular systems.

Role of CBS and Bateman Domains in Phosphorylation-Dependent Regulation of a CLC Anion Channel

“…(48). PQR files were generated using the PDB2PQR program (49). A negatively charged pocket between the two CLH-3b Bateman domains is shown in red.…”

Mimotope mapping as a complementary strategy to define allergen IgE-epitopes: Peach Pru p 3 allergen as a model☆

“…SES areas and relative accessibility values of each residue with respect to reference data were calculated with Arvomol 4.0 (Pacios, 1994) as explained elsewhere (Pacios, 2001). The electrostatic Poisson-Boltzmann (PB) potential mapped onto the protein surface was obtained with APBS 0.4.0 (Baker et al, 2001) assigning AMBER99 (Wang et al, 2004) atomic charges and radii, including hydrogens that were added with PDB2PQR (Dolinsky et al, 2004). Fine (0.50 A spacing) grids around the 1293 resulting atoms were used to solve the nonlinear PB equation in sequentialfocusing multigrid calculations in a mesh of 97 points per dimension at 298.15 K with dielectric constants 2 for the protein and 78.54 for water.…”

A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling

“…Before QM/MM calculations, several preparation steps were performed: hydrogen atoms were added using pdb2pqr package 13 version 2.1.1 using CHARMM force field version 27 14 , pH=7; hydrogen atoms were equilibrated by energy minimization in NAMD package 15 , version 2.11. The retinal chromophore was bound to the lysine residue Lys226, whole lysine + retinal system was parameterized in CHARMM force field 16 .…”