Tag
Molecular Modeling
Molecular Modeling UCSF ChimeraX Tutorial for Beginners: Load, Inspect and Clean a Protein Structure Learn UCSF ChimeraX in one sitting: fetch a PDB entry, master the 12 core commands, then clean the structure for docking or… Dr. Abdul Rajjak Shaikh 13 min read Updated 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… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling 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… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling 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… Dr. Abdul Rajjak Shaikh 11 min read Updated