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Package: pdb2pqr (1.8+dfsg-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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Download for all available architectures
Architecture Package Size Installed Size Files
alpha (unofficial port) 317.7 kB2,444.0 kB [list of files]
amd64 317.6 kB2,381.0 kB [list of files]
armel 309.1 kB2,347.0 kB [list of files]
armhf 311.6 kB2,295.0 kB [list of files]
hppa (unofficial port) 319.1 kB2,343.0 kB [list of files]
hurd-i386 316.0 kB2,367.0 kB [list of files]
i386 315.6 kB2,367.0 kB [list of files]
m68k (unofficial port) 315.2 kB2,288.0 kB [list of files]
mips 306.2 kB2,414.0 kB [list of files]
mipsel 308.0 kB2,414.0 kB [list of files]
powerpc 314.8 kB2,383.0 kB [list of files]
powerpcspe (unofficial port) 315.4 kB2,383.0 kB [list of files]
ppc64 (unofficial port) 315.8 kB2,440.0 kB [list of files]
s390x 315.7 kB2,409.0 kB [list of files]
sh4 (unofficial port) 329.9 kB2,395.0 kB [list of files]
sparc 306.2 kB2,373.0 kB [list of files]
sparc64 (unofficial port) 307.7 kB2,406.0 kB [list of files]
x32 (unofficial port) 318.8 kB2,356.0 kB [list of files]