Structure-based results you can defend.
Docking, molecular dynamics and structure analysis — set up, run and interpreted by a structural bioinformatician, with the limits of every result spelled out.
Who this is for
You’re a researcher, lab, or biotech team with a structure-based question — a target to screen against, a complex to simulate, a binding hypothesis to test — but you don’t have the time, the pipeline, or the in-house computational expertise to do it reliably.
You’ve maybe tried docking yourself and weren’t sure whether to believe the numbers. That’s exactly the gap I fill: I do the computational work, and I tell you honestly what it does and doesn’t show.
A good fit if
- You have a target structure (or a usable homolog) and a real question about it.
- You want results you can put in a grant, a paper, or a go/no-go decision.
- You’d rather hear “this method won’t answer that” than get a number that looks confident.
- You need the work documented well enough that a reviewer could follow it.
Not a fit if
- You need bench work — assays, synthesis, crystallography.
- You want a guarantee that the screen will produce an active compound.
- You need someone to sign off on results they didn’t produce.
- You want the cheapest possible run rather than one you can defend.
How I can help
Strategy call
A focused 30-minute call to talk through your project: which approach fits your question, what’s feasible, and what it would take. You leave with a clear plan whether or not we work together further.
A concrete recommendation and realistic expectations — no wasted compute.
You get
- A recommended approach for your question
- A written summary of the call
- A rough scope and cost if you want to proceed
Docking / virtual screening
End-to-end structure-based screening: target prep, docking, pose analysis, and a ranked, interpreted shortlist — with honest notes on confidence and where validation matters most.
A defensible, prioritised candidate list — not a raw score dump.
You get
- Prepared receptor and ligand files
- Ranked poses with interaction analysis
- Publication-ready figures
- A written report: methods, parameters, caveats
Molecular dynamics study
Setting up and running MD through to analysis — stability, interactions, binding free energy (MM-GBSA where appropriate) — with a clear written interpretation of what it means for your question.
Simulation evidence you can put in a paper or a decision, properly contextualised.
You get
- Full system setup and simulation files
- RMSD, RMSF, contact and H-bond analysis
- Binding free energy estimates where justified
- A written report with plots and interpretation
Done-for-you research support — larger or ongoing projects
For projects that need the full pipeline or sustained support — structure prep, docking, MD, and interpretation combined, scoped to your goal. A computational collaborator without an in-house hire. Priced per project or as a monthly retainer, agreed before we start.
How it works
- You get in touch. Book a strategy call or email me a short description of the project.
- I scope the work. You get a written plan, a timeline and a fixed price before anything starts. No open-ended hourly billing.
- You send me what I need. Usually a target structure or PDB/UniProt ID, your compounds as SMILES or SDF, any known actives, and what you’re trying to decide.
- I run the work. With a checkpoint partway through, so you can redirect before the whole budget is spent.
- You get results and an interpretation. What they show, how confident we should be, what to do next — plus the underlying files, so the work is reproducible.
Get started
Book a strategy call, or email me a short description of your project — the target, the compounds, and the decision you’re trying to make. I’ll tell you whether I can help.
or email admin@structbiotools.com