Including explicitly treated interfacial water molecules improved the free energy calculation for the binding of SARS-CoV-2 spike RBD and antibodies.

Published in Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2023.2199336

Highlights：

1. Including explicitly treated interfacial water molecules improved the free energy calculation for the binding of SARS-CoV-2 spike RBD and antibodies.

2. Developed a screening method for interfacial water based on water molecular dynamics features and applied it to MM/PBSA.

3. Structural and energetic analyses confirmed the critical roles played by interfacial water in protein-protein binding.

4. Compromised interaction with interfacial water molecules partly explains the immune escape of the Omicron variant.

5. Generalizability that the calculation and analyzing can be extended to all receptor-ligand hydration system.

Typical usage:

Execute the following command in terminal. Ensure all Python packages meet the runtime requirements.

python /local_path/HyHOH/gmx/pygmx/main.py -tpr ../md_0.tpr -xtc ../md_0.xtc -ri 194 622 -li 1 193 -fm normal -rm hyhoh -t 5000 10000 20

-ri The residues index of receptor

-li The residues index of ligand

-fm Sampling method for MD frames, can be 'normal', 'most'(our method).

-rm Methods to run MM/PBSA, can be 'normal', 'hyhoh'(Our method), 'dsthoh'.

-t Four numeric with spaces separate to specify the sampling interval. [begin, end, interval, frames_per_ps] in ps. This option can be ignored if a frames indexing list was assigned in source code by manual

IF any question you can contact contributors of this repository, or new open a new issue.

LICENSE:

GNU General Public License v3.0