Molecular Modeling
How to Define the Simulation Box in GROMACS with gmx editconf (Cubic vs Dodecahedron): A Step-by-Step Guide
Set your GROMACS simulation box with gmx editconf. Choose cubic or dodecahedron, pick the right -d distance, and cut roughly 29 percent of your run time.
Homology Modelling Tutorial for Beginners: Build a Protein Structure with SWISS-MODEL (Step by Step)
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.
How to Predict a Protein Structure with AlphaFold (ColabFold, No Install): A Beginner’s Guide
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.