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.
This package is distributed via Conda. To install it, run the following command:
conda install -c conda-forge -c omnia -c michellab -c essexlab protocallerThe development version can be installed with this command (use with caution):
conda install -c conda-forge -c omnia -c michellab -c essexlab/label/dev protocallerThe newest version (1.1.1) is highly recommended due to some compatibility issues with the most recent versions of BioSimSpace and Modeller.
IMPORTANT: Please note that some recent (10.04.2020) changes to the Protein Data Bank broke compatibility with ProtoCaller. As there seem to be some unresolved issues with the database, there is a temporary hotfix for ProtoCaller that will be subject to change as the matter progresses further. Until then, please use the current development version:
conda install -c conda-forge -c omnia -c michellab -c essexlab/label/dev protocaller=1.1.2Full docstring documentation can be found here. There are also a few examples which you can run to see how ProtoCaller works.