🧬
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