Blog

Turn a docked pose into a figure your supervisor accepts. Real PyMOL commands for cartoon-plus-sticks, labelled H-bonds, and a 300 dpi ray-traced render.

Stop copy-pasting em.mdp and md.mdp. Learn which GROMACS .mdp parameters you must choose deliberately, which to leave at defaults, and what breaks when you get them wrong.

Decode the GROMACS errors beginners actually hit: LINCS warnings, PBC artifacts, rtp mismatches and cut-off failures. Read the fix for each message.

Estimate protein-ligand binding free energy from a finished GROMACS trajectory with the free gmx_MMPBSA tool. Follow the step-by-step MM-PBSA workflow now.

Learn to run blind docking in AutoDock Vina to find an unknown binding site, from sizing a whole-protein box to clustering poses. Start the step-by-step guide.

Compare AutoDock Vina and AutoDock4 on scoring, speed, setup, and accuracy so you pick the right docking engine for your thesis. Read the guide before you start.

Turn any AutoDock Vina or PyRx docking pose into a publication-ready 2D interaction diagram with free tools. Follow the LigPlot+ and PLIP workflow now.

Learn to choose between an experimental PDB structure, a SWISS-MODEL homology model, or AlphaFold for docking and MD, judged on coverage, confidence and fit.

Learn to clean a raw PDB for MD: rebuild missing loops, add hydrogens, and fix His, Asp and Cys protonation so your simulation does not crash.

Validate your AlphaFold or homology model with a Ramachandran plot and MolProbity before you waste compute on docking. Learn every score and threshold.