Molecular Modeling

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.

Build a 3D protein model from sequence with SWISS-MODEL, no install. Learn to pick a template and read GMQE and QMEANDisCo before you dock.

Fold your protein sequence with AlphaFold in ColabFold, free and no install. Learn to read pLDDT and PAE so you know if the model is good enough to dock.

Write a docking methods section a reviewer accepts. Get the reporting checklist plus a worked, copy-adaptable AutoDock Vina example.

Set the AutoDock Vina grid box the right way: find the binding-site center, pick a box size in Angstroms, and stop guessing coordinates. Start docking today.

Run a full GROMACS molecular dynamics simulation on Google Colab’s free GPU, no local install. Set up the runtime, install GROMACS, and save your trajectory.

Run PCA on a GROMACS trajectory with gmx covar and gmx anaeig to extract the dominant collective motions. Start building thesis-grade figures today.

Measure compactness, solvent exposure and H-bonds from a GROMACS trajectory with gmx gyrate, gmx sasa and gmx hbond. Start analyzing your MD run today.

Learn how to build a GROMACS-ready ligand topology. Compare CGenFF, ACPYPE and ATB, then prepare a defensible protein-ligand system step by step.