Blog

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.

Pick a scoped, defensible molecular docking project you can finish with free tools and public data. Start building your thesis today.

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.

Decide which force field to pick at the GROMACS pdb2gmx step. Compare CHARMM36, AMBER and OPLS, and learn to justify your choice in a thesis.