Structure & drug discovery
Structural Bioinformatics
We analyse experimental and predicted protein structures to answer specific questions: is this model good enough for docking, where are the binding sites, how do two structures differ, and where do variants of interest fall in three dimensions.
Who it is for
- Groups interpreting variants or mutations at the structural level
- Drug-discovery projects choosing a target structure
- Labs comparing homologues, mutants or conformations
What you send us
- PDB IDs or structure filesExperimental structures in PDB or mmCIF format.
- SequencesFor retrieving or generating predicted models.
- Variant or residue listsPositions to map and assess.
What you receive
- Analysis report with figures
- PyMOL sessions and annotated structure files
- Binding-site, contact and variant tables
- Methods section
Methodology
How the work runs
Each step is agreed with you and documented. Typical tools: AlphaFold DB · ColabFold · PyMOL (open source) · Mol* · fpocket · PLIP · TM-align
- ScopingThe structural question, the proteins involved and how the answer will be used.
- Structure selectionExperimental structures assessed by resolution, completeness and ligand state; predicted models assessed by pLDDT and PAE.
- AnalysisBinding-site detection, interaction profiling, superposition (RMSD, TM-score) and solvent accessibility, as the question requires.
- Variant mappingPositions mapped to the structure with local environment, conservation and contacts reported.
- ReportFigures, structure sessions, tables and a methods section.
Quality controls
Checks applied to every project
- Model confidence (pLDDT, PAE) reported for every predicted region used
- Missing residues and alternate conformations flagged
- Superposition reported with both RMSD and TM-score
- Conclusions limited to regions with adequate structural evidence
Scope and limits
What the work can and cannot show
- A structural argument for a variant’s effect is evidence to weigh, not proof of pathogenicity.
- Low-confidence regions of predicted models are not used for detailed conclusions.
- Research use only: results are not a clinical or diagnostic report.
Free quote
Start a Structural project.
Describe your data and questions. We reply with questions or a written quote.
It depends on the data type, the number of samples and the depth of interpretation you need. Every project receives a written quote with scope, deliverables, price and delivery date after a short exchange about your data and questions. The quote is free and carries no obligation.
For most single-chain proteins and many complexes we can generate or retrieve an AlphaFold model and assess where it is reliable. Regions with low confidence are reported as such rather than interpreted.
Data are used only for your project, transferred through a channel you approve and deleted at the end of the engagement on request. We will sign your institution’s confidentiality agreement before any data are shared.
Yes. You receive a methods section with software versions and parameters, and every figure can be regenerated from the delivered code. Authorship or acknowledgement follows your field’s norms and is agreed at the start.
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