Tag
Protein-Protein Docking
Molecular Modeling MD Simulation of a Protein-Protein Complex in GROMACS Take a docked or AlphaFold-Multimer complex through GROMACS, keep both chains whole, and test the interface with RMSD, contacts and H-bonds. Start… Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling PDBePISA Tutorial: Analyse a Protein-Protein Interface Run PDBePISA on a crystal or docked complex, read interface area, ΔiG, P-value, H-bonds and CSS, and report them correctly. Follow the… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Calculate Protein-Protein Binding Affinity Score your docked protein-protein complex with PRODIGY and HawkDock MM/GBSA, read dG and Kd correctly, and learn why a docking score is… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Do Protein-Protein Docking Online (ClusPro, HDOCK and HADDOCK): A Step-by-Step Guide for Beginners Dock two proteins in a browser with ClusPro, HDOCK or HADDOCK. Prepare your files, run the job, and learn which model to… Dr. Abdul Rajjak Shaikh 17 min read Updated