Guides to docking, molecular dynamics and drug discovery
Plain-language tutorials written for students and researchers who want to understand the methods, not just run them.
Prepare the protein and ligands, define the binding site, validate by re-docking, dock your compounds, then inspect interactions instead of trusting scores alone.
GROMACS tutorialGROMACS Protein–Ligand MD Simulation WorkflowBuild topologies, solvate and neutralise, minimise, equilibrate in NVT then NPT, run production, then correct periodic boundaries before analysis.
MD analysis guideHow to Interpret MD Simulation Results: RMSD, RMSF, Rg, SASALook for convergence, not single numbers. Combine several metrics before concluding that a ligand is stably bound.
Free-energy guideMM/PBSA Binding Free Energy Explained for BeginnersMM/PBSA estimates binding energy from MD snapshots. It ranks similar ligands reasonably well but is not an exact measure of affinity.
ADME guideADME and Drug-Likeness: Lipinski's Rule of Five ExplainedADME describes absorption, distribution, metabolism and excretion. Drug-likeness rules are quick filters that remove compounds unlikely to behave like oral drugs.
Virtual screening guideVirtual Screening Workflow: From Library to Hit ListPrepare the target and library, filter by properties, validate the docking setup, dock, then rank, cluster and inspect before choosing compounds to test.
Looking up a term? Try the computational drug discovery glossary.