Service arm B
Structure-based small-molecule work
You have a target structure and want to decide where to start on the small-molecule side: is the pocket actually tractable, which compounds come first, how can an existing starting compound be improved.
Projects that fit this work
- A structure exists and the binding site can be defined.
- A compound list or library preference can be specified.
- There is a route to testing the result experimentally.
What we need from you to start
- The target structure (PDB ID or file).
- The pocket or region of interest.
- A compound list or library preference.
- Any starting compound and known activity data.
The work itself
| Service | Input | Output | Scope limit |
|---|---|---|---|
| Molecular docking | Target structure and compound list | Ranked poses, score table, interaction fingerprints | A docking score is not a binding free energy. |
| Binding-site and druggability analysis | Target structure | Pocket definition, volume, druggability assessment, hotspot map | — |
| Virtual screening for hit discovery | Target structure and library preference | Filtered and ranked hit list, diversity clustering | A filtering and ranking output; no physical hit is guaranteed. |
| Structure-based optimisation support | Target and starting compound | Analog suggestions with interaction-based rationale | — |
Out of scope
These items are listed deliberately: we write down what is not included so the quote holds no surprises.
- Compound synthesis and procurement.
- Biochemical or cellular assay work.
- ADMET profiling and solid form prediction — external provider items.
- Presenting a docking score as an affinity.
Terms used on this page
New to the field? Start here. The explanations are deliberately short.
- target
- The protein you are working on — the molecule you want to engage, block or detect.
- structure
- The three-dimensional shape of a protein — a map of where each atom sits.
- docking
- Computing how a small molecule might sit in a pocket on the target.
- druggability
- How suitable a pocket is for being targeted by a drug-like molecule.
- virtual screening
- Filtering a large set of compounds on a computer to surface the most promising ones.
- affinity
- How tightly two molecules hold on to each other. It is measured in the lab, not computed.
- computational
- Work done on a computer. It is not an experiment; it shows which candidate is worth testing.
- PDB
- The public database of experimentally solved protein structures.
Describe your target briefly and we will settle the scope together.
The first message never asks for confidential sequences, unpublished structures or sensitive files. Technical detail follows an appropriate confidentiality process.