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pdb2pqr

Preparation of protein structures for electrostatics calculations

Description

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations. It thus provides a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include:
 * Adding a limited number of missing heavy atoms to biomolecular structures
 * Determining side-chain pKas
 * Placing missing hydrogens
 * Optimizing the protein for favorable hydrogen bonding
 * Assigning charge and radius parameters from a variety of force fields

This package also includes PropKa, a tool to modify the protonation state of protein structures in the Protein Data Bank (PDB) format to match a given pKa value. It can also be used to refine NMR structures, which often yield inaccurate pKa values for some residues.

Homepage

http://pdb2pqr.poissonboltzmann.org/pdb2pqr/


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