URL: https://server.poissonboltzmann.org/pdb2pqr

Licence: Free and open-source license

PDB2PQR is a python software package that automates many of the common tasks of preparing structures for continuum solvation calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format.

Some of the other functionalities of PDB2PQR include:

  • adding a limited number of missing heavy (non-hydrogen) 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.

Webserver: https://server.poissonboltzmann.org/pdb2pqr

Application/Keywords: Structure preparation, pKa calculations, Force field parameters, PQR file generation