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.

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  1. Jiang, Yi; Xie, Yang; Ying, Jinyong; Xie, Dexuan; Yu, Zeyun: SDPBS web server for calculation of electrostatics of ionic solvated biomolecules (2015)
  2. Harris, Robert C.; Mackoy, Travis; Fenley, Marcia O.: A stochastic solver of the generalized Born model (2013)
  3. Aksoylu, Burak; Bond, Stephen D.; Cyr, Eric C.; Holst, Michael: Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation (2012)
  4. Ho, Kenneth L.; Greengard, Leslie: A fast direct solver for structured linear systems by recursive skeletonization (2012)
  5. Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin: Variational multiscale models for charge transport (2012)
  6. Zheng, Qiong; Yang, Siyang; Wei, Guo-Wei: Biomolecular surface construction by PDE transform (2012)
  7. Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander: An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics (2011)
  8. Fernández, Ariel: Nanoscale thermodynamics of biological interfacial tension. (2011)
  9. Zheng, Qiong; Chen, Duan; Wei, Guo-Wei: Second-order Poisson-Nernst-Planck solver for ion transport (2011)
  10. Zhang, Xiaoyu; Bajaj, Chandrajit L.; Kwon, Bongjune; Dolinsky, Todd J.; Nielsen, Jens E.; Baker, Nathan A.: Application of new multiresolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity (2006)