Skip to content
A pDynamo-based toolkit for protonation state calculations in proteins
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
ContinuumElectrostatics
doc
extensions
parameters
tests
.gitignore
INSTALL
Licence_CeCILL_V2-en.txt
Licence_CeCILL_V2-fr.txt
README.md
dependencies
logo.png

README.md

Pcetk logo

Pcetk (a pDynamo-based continuum electrostatic toolkit) is a Python module extending the pDynamo library with a microstate model for the calculation of proton binding energetics in proteins.

The module links pDynamo to the external solver of the Poisson-Boltzmann equation, extended-MEAD, which is used for the calculation of electrostatic energy terms. The calculation of protonation states and titration curves is done with custom analytic or Monte Carlo routines or, optionally, through an interface to the external sampling program, GMCT.

Author: Mikolaj Feliks <mikolaj.feliks@gmail.com>

Released under the CeCILL Free Software License, a French equivalent of the GNU General Public License. More information can be found in Licence_CeCILL_V2-en.txt or Licence_CeCILL_V2-fr.txt (in French).

Key features of Pcetk

  • Extensible framework for studying protein titration
  • User interface is a Python script
  • Close integration with pDynamo
  • Computationally intensive parts of code implemented in C/Cython
  • Improved treatment of polyprotic sites: histidines or polyprotic ligands
  • Analytic calculation of protonation states (for small proteins)
  • Custom Metropolis Monte Carlo sampling algorithm (for large proteins)
  • Calculations of substate energies
  • Automatic generation of titration curves
  • Parallel calculation of electrostatic energy terms with MEAD

Citation

If you use Pcetk in your work, please cite:

Mikolaj Feliks & Martin Field, "Pcetk: A pDynamo-based Toolkit for Protonation State Calculations in Proteins.", J. Chem. Inf. Model. 2015, 55, 2288-2296

Bibtex

@article{ Feliks2015,
author  = {Feliks, Mikolaj and Field, Martin},
title   = "{{Pcetk}: A pDynamo-based Toolkit for Protonation State Calculations in Proteins}",
journal = {J. Chem. Inf. Model.},
year    = {2015},
volume  = {55},
pages   = {2288-2296},
url     = {http://dx.doi.org/10.1021/acs.jcim.5b00262},
}

Installation instructions

Required software and libraries:

  • pDynamo 1.8.0
  • Extended-MEAD 2.3.0
  • Python 2.7 (including header files; python2.7-dev package in Debian)
  • PyYAML 3.10 (python-yaml package in Debian)
  • GNU toolchain (GCC, make)

Optionally:

  • Cython 0.15.1 (for recompiling Cython sources)
  • GMCT 1.2.3

For proper functioning, Pcetk requires two programs from the Extended-MEAD package, namely my_2diel_solver and my_3diel_solver. Download Extended-MEAD and follow its installation instructions. In the future, the toolkit may switch to a custom Poisson-Boltzmann solver.

In the next step, clone the newest repository of Pcetk from GitHub:

$ git clone https://github.com/mfx9/pcetk.git

Some modules are written in C/Cython and have to be compiled before they can be used. These modules include StateVector, EnergyModel and MCModelDefault.

Go to extensions/cython and edit the first line of Makefile. The PDYNAMO_CORE variable should point to the location of pDynamo. After editing the file, run make install.

$ cd extensions/cython
$ vi Makefile
  (... now edit the file ...)
$ make install

See the manual for more details.

At this point, the installation is complete. Before Pcetk can be used, set or update the PDYNAMO_PCETK and PYTHONPATH variables:

$ export PDYNAMO_PCETK=/home/mikolaj/devel/pcetk
$ export PYTHONPATH=${PDYNAMO_PCETK}:${PYTHONPATH}

Manual

Please, see the manual for detailed instructions and examples of use.

Auxiliary software

Extended-MEAD was written by Donald Bashford and extended by Timm Essigke and Thomas R. Ullmann. GMCT was written by Matthias G. Ullmann and Thomas R. Ullmann. pDynamo was written by Martin Field and collaborators.

You can’t perform that action at this time.