ProtoCaller
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Full automation of relative protein-ligand binding free energy calculations in GROMACS
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.