PDB2PQR

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.


References in zbMATH (referenced in 19 articles )

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  1. Cooper, Christopher D.; Barba, Lorena A.: Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code (2016)
  2. Xie, Dexuan; Jiang, Yi: A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules (2016)
  3. Jiang, Yi; Xie, Yang; Ying, Jinyong; Xie, Dexuan; Yu, Zeyun: SDPBS web server for calculation of electrostatics of ionic solvated biomolecules (2015)
  4. Tu, Bin; Xie, Yan; Zhang, Linbo; Lu, Benzhuo: Stabilized finite element methods to simulate the conductances of ion channels (2015)
  5. Ying, Jinyong; Xie, Dexuan: A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule (2015)
  6. Shu, Yu-Chen; Chern, I-Liang; Chang, Chien C.: Accurate gradient approximation for complex interface problems in 3D by an improved coupling interface method (2014)
  7. Xie, Dexuan: New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics (2014)
  8. Harris, Robert C.; Mackoy, Travis; Fenley, Marcia O.: A stochastic solver of the generalized Born model (2013)
  9. Liu, Jinn-Liang: Numerical methods for the Poisson-Fermi equation in electrolytes (2013)
  10. Aksoylu, Burak; Bond, Stephen D.; Cyr, Eric C.; Holst, Michael: Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation (2012)
  11. Ho, Kenneth L.; Greengard, Leslie: A fast direct solver for structured linear systems by recursive skeletonization (2012)
  12. Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin: Variational multiscale models for charge transport (2012)
  13. Zheng, Qiong; Yang, Siyang; Wei, Guo-Wei: Biomolecular surface construction by PDE transform (2012)
  14. Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander: An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics (2011)
  15. Fernández, Ariel: Nanoscale thermodynamics of biological interfacial tension. (2011)
  16. Zheng, Qiong; Chen, Duan; Wei, Guo-Wei: Second-order Poisson-Nernst-Planck solver for ion transport (2011)
  17. Dolinsky, Todd J.; Czodrowski, Paul; Li, Hui; Nielsen, Jens E.; Jensen, Jan H.; Klebe, Gerhard; Baker, Nathan A.: PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. (2007)
  18. 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)
  19. Dolinsky, Todd J.; Nielsen, Jens E.; Mccammon, James Andrew; Baker, Nathan A.: PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. (2004)