Computational drug discovery for students and thesis projects

Online protein–ligand molecular docking: structure and ligand preparation, binding-site definition, pose ranking, interaction analysis and a full report.

In silico ADME and drug-likeness prediction: Lipinski and Veber rules, physicochemical descriptors, solubility, permeability and toxicity alerts for compound prioritisation.

GROMACS molecular dynamics simulation of protein–ligand complexes with equilibration, production run and full trajectory analysis (RMSD, RMSF, Rg, SASA, H-bonds, PCA, FEL).

Ligand preparation for docking and virtual screening: standardisation, protonation and tautomer states, 3D generation, energy minimisation and format conversion.

Prepare the protein and ligands, define the binding site, validate by re-docking, dock your compounds, then inspect interactions instead of trusting scores alone.

Look for convergence, not single numbers. Combine several metrics before concluding that a ligand is stably bound.