Computational services

We run your simulations for you

You don't have the computing power, the installed software or the time? We take charge of your simulations and deliver the analysed results.

Périmètre des prestations. Nous réalisons uniquement de la modélisation et de l'analyse computationnelle. Nous ne réalisons pas de tests expérimentaux en laboratoire (synthèse chimique, essais biologiques). Les résultats prédits sont des hypothèses qui doivent être validées expérimentalement avant toute conclusion thérapeutique.
Our services

Six molecular modelling services

Each service can be performed independently or combined into a complete project, from initial screening to article writing.

Molecular docking

You provide a target and a list of molecules: we prepare the files, define the grid, run the docking and deliver the scores, poses and analysed interactions.

  • Receptor and ligand preparation (PDBQT)
  • AutoDock Vina docking, optimised parameters
  • Validation by redocking and RMSD calculation
  • PLIP interaction analysis

Virtual screening

Screening of compound collections (ZINC, PubChem, in-house libraries) with ranking and selection of priority hits.

  • Library assembly and preparation
  • Automated, parallelised screening
  • Clustering of hits by chemical similarity
  • Final ranking and prioritisation

Molecular dynamics

Simulations from 100 ns to several microseconds to assess the stability of your complexes and refine docking predictions.

  • System preparation (solvation, ions)
  • Minimisation, equilibration, production
  • RMSD, RMSF, hydrogen bond analysis
  • Binding free energy (MM/PBSA, MM/GBSA)

ADMET filtering

Assessment of pharmacokinetic and toxicological properties to eliminate problematic compounds before any laboratory testing.

  • Absorption, distribution, metabolism, excretion
  • Lipinski's and Veber's rules
  • Oral bioavailability prediction
  • Structural toxicity alerts

Structure modelling

Obtaining a 3D structure when no experimental structure is available for your target.

  • AlphaFold2 / ESMFold prediction
  • Homology modelling (MODELLER)
  • Quality assessment (pLDDT, PAE, Ramachandran)
  • Preparing the model for docking

LaTeX scientific writing

Professional formatting of your articles, theses and reports, complying with scientific journal standards.

  • IMRaD structuring (Introduction, Methods, Results, Discussion)
  • booktabs tables and siunitx units
  • Multi-panel figures with subcaption
  • BibTeX bibliography and journal compliance
Process

How a service engagement works

Scoping

You describe the biological question, the target and the molecules of interest. We assess feasibility and required computation time.

Quotation

We send you a quotation specifying the scope, the deadline and the expected deliverable.

Execution

File preparation, running the simulations, quality control and regular progress updates.

Delivery

Analysed results, figures, tables and a reproducible methodological report. Raw files are provided.

Quote request

Describe your project

The more precise your description, the more relevant our quote will be. All fields marked with an asterisk are required.

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Frequently asked questions

What to know before entrusting us with a project

How long does a docking take?

It depends on the number of molecules and the size of the active site. A few dozen molecules take hours; screening 100,000 compounds requires several days of computation. We specify the deadline in the quote.

Do you provide the raw files?

Yes. We systematically deliver the raw output files, the scripts used and a methodological report allowing the analysis to be reproduced.

Can I publish the results?

Yes, the results belong to you. We can be acknowledged or listed as co-authors depending on your level of involvement, to be discussed when quoting.

Do you guarantee the activity of the molecules?

No. Docking predicts a theoretical affinity, not real biological activity. No computational method replaces experimental testing. We provide hypotheses to be tested, not proof of efficacy.

Do you work on confidential data?

Yes, on request and after signing a non-disclosure agreement (NDA). We can also work on your own servers if your data cannot leave your institution.

A project to entrust to us?

Describe your needs and we will get back to you with a proposal adapted to your context and budget.