Drug Discovery Docking & Dynamics
Budget: $30 – $250 USD
I need a complete in-silico workflow that will let me pinpoint promising drug candidates, map out their protein-protein, protein-ligand and protein-peptide interactions, and clarify the underlying molecular mechanisms. The work spans virtual screening, molecular docking, full molecular dynamics (MD) production runs and post-simulation analytics.
Here is what I am after:
• Drug discovery screening: set up and run docking (rigid and flexible) against my target(s), ranking hits with appropriate scoring functions.
• Protein-protein, protein-ligand and protein-peptide interaction studies: calculate binding energies, key residue contacts and interaction fingerprints.
• Molecular dynamics simulation analysis: perform equilibrium checks (RMSD, RMSF, Rg), free-energy estimates (MM/PBSA or equivalent) and provide trajectory visualisations.
• ADMET profiling and QSAR modelling: predict pharmacokinetic/tox profiles and build a preliminary quantitative structure–activity relationship model for the top compounds.
Deliverables must include all input files, raw trajectories, processed data tables, scripts or notebooks used, clear figure panels and a concise report tying the results together so I can reproduce or extend the work with minimal effort. Tools such as AutoDock Vina, GROMACS, SwissADME or similar are fine as long as the methodology is documented.
If this scope is clear and you are comfortable running the full pipeline from docking through MD and ADMET/QSAR evaluation, I’m ready to move forward.
Here is what I am after:
• Drug discovery screening: set up and run docking (rigid and flexible) against my target(s), ranking hits with appropriate scoring functions.
• Protein-protein, protein-ligand and protein-peptide interaction studies: calculate binding energies, key residue contacts and interaction fingerprints.
• Molecular dynamics simulation analysis: perform equilibrium checks (RMSD, RMSF, Rg), free-energy estimates (MM/PBSA or equivalent) and provide trajectory visualisations.
• ADMET profiling and QSAR modelling: predict pharmacokinetic/tox profiles and build a preliminary quantitative structure–activity relationship model for the top compounds.
Deliverables must include all input files, raw trajectories, processed data tables, scripts or notebooks used, clear figure panels and a concise report tying the results together so I can reproduce or extend the work with minimal effort. Tools such as AutoDock Vina, GROMACS, SwissADME or similar are fine as long as the methodology is documented.
If this scope is clear and you are comfortable running the full pipeline from docking through MD and ADMET/QSAR evaluation, I’m ready to move forward.