PDB2PQR -- An automated pipeline for the setup of Poissonx96Boltzmann electrostatics calculations

URL:
http://pdb2pqr.sourceforge.net/
What you can do:
Automates many of the common tasks of preparing structures for continuum electrostatics calculations.
Highlights:
  • The PDB2PQR web server addresses the need for electrostatic field calculations.
  • Here we report the significantly expanded PDB2PQR that includes the following features: robust standalone command line support, improved pK(a) estimation via the PROPKA framework, ligand parameterization via PEOE_PB charge methodology, expanded set of force fields and easily incorporated user-defined parameters via XML input files, and improvement of atom addition and optimization code.
  • These features are available through a new web interface which offers users a wide range of options for PDB file conversion, modification and parameterization.
Keywords:
  • electrostatics calculations
  • Continuum solvation models
  • protein structures
  • Mathematical Computing
Literature & Tutorials:
PubMed Link: PDB2PQR
2007 Update: PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
This record last updated: 05-27-2008
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