PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations.
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.
Dolinsky
Todd J
TJ
Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, 700 S. Euclid Avenue, Campus Box 8036, St Louis, MO 63110, USA.
Nielsen
Jens E
JE
McCammon
J Andrew
JA
Baker
Nathan A
NA
D030562:Databases, Protein; D006859:Hydrogen / Q000737:chemistry; D006860:Hydrogen Bonding; D020407:Internet; D008432:Mathematical Computing; D015394:Molecular Structure; D011506:Proteins / Q000737:chemistry*; D012984:Software; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity
D011506:Proteins; D012997:Solvents; D006859:Hydrogen