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protocaller / ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS
http://protocaller.readthedocs.io
GNU General Public License v3.0
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free-energies gromacs high-throughput ligand-binding molecular-dynamics-simulation python

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ProtoCaller

About

ProtoCaller is a Python library which enables controlled automation of relative protein-ligand binding free energy calculations in GROMACS. ProtoCaller uses a variety of tools to automate the free energy calculation process, such as: Biopython, BioSimSpace, CHARMM-GUI, (optionally) Modeller, Open Babel, ParmEd, PDB2PQR, pdbfixer, RDKit.

ProtoCaller can be run on both Linux and macOS. Installation is easy and performed through Conda. Please check the other sections for further information.

Installation

This package is distributed via Conda. To install it, run the following command:

.. code-block:: bash

conda install -c conda-forge -c omnia -c michellab -c essexlab protocaller

The development version can be installed with this command (use with caution):

.. code-block:: bash

conda install -c conda-forge -c omnia -c michellab -c essexlab/label/dev protocaller

The newest version (1.2.0) is highly recommended due to recent database overhauls in the Protein Data Bank.

Getting Started

Full docstring documentation can be found here <https://protocaller.readthedocs.io/en/latest/ProtoCaller.html>. There are also a few examples <https://protocaller.readthedocs.io/en/latest/Examples.html> which you can run to see how ProtoCaller works.