Protein-Protein Docking Study Needed

I am midway through a structural bioinformatics study that zeroes in on molecular docking, specifically the binding interface between two target proteins. The raw PDB structures have already been gathered; what I now need is a seasoned hand to carry the project from initial preparation through to an interpretable, publication-ready data set.

Your tasks will include preparing and refining the protein models, running protein–protein docking simulations, clustering and scoring the resulting poses, and interpreting the key interaction hotspots. You are welcome to deploy established platforms such as HADDOCK, ClusPro, RosettaDock, or a comparable toolchain you are comfortable with—just keep your workflow fully reproducible (command logs, parameters, and version numbers).

Deliverables
• Cleaned and pre-processed PDB files for both proteins
• Docking pipeline scripts or notebooks with step-by-step commands
• Ranked docking poses with interface‐specific energy scores
• Visualisations (PyMOL session or equivalent) highlighting critical contacts
• A concise report summarising methods, key findings, and recommended follow-up mutations or assays

I will consider the job complete once the results can be reproduced on my local machine and the report addresses all interaction hotspots with clear rationale. If this scope aligns with your expertise in structural bioinformatics, let’s proceed.