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[ Source: pdb2pqr  ]

Package: pdb2pqr (1.8-1)

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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 456.5 kB2,390.0 kB [list of files]
armel 446.7 kB2,342.0 kB [list of files]
armhf 435.7 kB2,289.0 kB [list of files]
i386 454.0 kB2,373.0 kB [list of files]
ia64 487.8 kB2,617.0 kB [list of files]
mips 440.7 kB2,399.0 kB [list of files]
mipsel 445.2 kB2,399.0 kB [list of files]
powerpc 456.6 kB2,380.0 kB [list of files]
s390 446.5 kB2,379.0 kB [list of files]
s390x 458.1 kB2,412.0 kB [list of files]
sparc 446.3 kB2,367.0 kB [list of files]