PROJECT DESCRIPTION
Monkeypox virus, also known as Mpox virus, is an emerging viral pathogen that requires continuous antiviral research due to its public health importance and potential for future outbreaks. Viral protease and replication-associated proteins are important computational targets for identifying small-molecule inhibitors that may interfere with viral replication and protein processing.
This project applies structure-based drug discovery, molecular docking, molecular dynamics simulation, ligand interaction analysis, and binding free energy calculation to identify potential inhibitors against Monkeypox main protease or related essential viral proteins. The project focuses on binding affinity, active-site stability, key residue interactions, and lead optimization for antiviral candidate selection.
PROJECT CONTENT
- Monkeypox viral protein structure preparation and refinement
- Active-site prediction and target residue identification
- Ligand library preparation and drug-likeness screening
- Molecular docking of antiviral candidates against Mpox main protease
- 2D and 3D interaction analysis of hydrogen bonds, hydrophobic contacts, and π-interactions
- Molecular dynamics simulation of top-ranked protein–ligand complexes
- RMSD, RMSF, Rg, SASA, and hydrogen bond stability analysis
- MM/GBSA or MM/PBSA binding free energy calculation
- Residue-wise energy decomposition for key binding residues
- ADMET, toxicity, and antiviral lead-likeness evaluation
- Lead optimization based on docking score, MD stability, and binding energy profile