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[ Source: pdb2pqr  ]

Package: pdb2pqr (2.1.1+dfsg-2)

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Preparation of protein structures for electrostatics calculations

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.

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Architecture Package Size Installed Size Files
amd64 364.5 kB2,792.0 kB [list of files]
arm64 356.8 kB2,815.0 kB [list of files]
armel 350.6 kB2,775.0 kB [list of files]
armhf 352.1 kB2,663.0 kB [list of files]
i386 368.3 kB2,768.0 kB [list of files]
mips 359.4 kB3,039.0 kB [list of files]
mips64el 365.3 kB3,099.0 kB [list of files]
mipsel 363.3 kB3,039.0 kB [list of files]
ppc64el 365.0 kB2,975.0 kB [list of files]
s390x 364.4 kB2,947.0 kB [list of files]