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.
Please see doc/userguide.html for the documentation index and COPYING for license information.
Please see doc/programmerguide.html for information on working with the PDB2PQR code.
PDB2PQR can use PROPKA to protonate the structure it converts. PROPKA is
packaged along with the PDB2PQR in this package.
-- Manuel Prinz Thu, 21 Jun 2012 15:57:01 +0200
The Debian package of PDB2PQR currently does not provide the parts that are
necessary to run PDB2PQR as a web service. If you think that the PDB2PQR
web service should be available as a
Please see the programmer's guide (doc/programmerguide.html) for a discussion on how to add your own functionality to PDB2PQR.
Additionally, the "template" file is a template for interfacing with PDB2PQR.
PDB2PQR(1) PDB2PQR Manual PDB2PQR(1)
pdb2pqr - Genera
PROPKA(1) PROPKA Manual PROPKA(1)
propka - Protona
PSIZE(1) PDB2PQR Manual PSIZE(1)
psize - Get dime
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