Post processing MD trajectory Water Analysis
- RDF of water molecules in specified regions
- Residence time calculations
- 3D water density maps
Protein-Ligand Interaction
- Percentage of Specific interaction (Hydrogen bond and hydrophobic interaction tracking)
- Atom wise Contact maps of Ligand over time
- Ligand residence time
- Ligand torsional angle changes
The aim of this repository is to provide a transparent and reproducible framework for the analyses presented in the manuscript "Hydrophobicity and Water-Mediated Interactions Modulate Residue Contributions to Binding Dynamics of Viral Protease-Hyperin Complexes"
Pushyaraga P. Venugopal, Omkar Singh, Vinod, "Hydrophobicity and water-mediated interactions modulate residue contributions to binding dynamics of viral protease-hyperin complexes", Journal of Molecular Liquids, Volume 438, Part A, 2025, 128684, ISSN 0167-7322, https://doi.org/10.1016/j.molliq.2025.128684. (https://www.sciencedirect.com/science/article/pii/S0167732225018616)