Topic
Molecular Modeling
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 MD Simulation at Different Temperatures in GROMACS Set up a 300 K vs 350 K vs 400 K thermal stability study in GROMACS, keep the runs comparable, and read… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling SAVES Server Tutorial: ERRAT, Verify3D and PROCHECK Upload a homology or AlphaFold model to SAVES v6.1 and learn to read ERRAT, Verify3D and PROCHECK scores. Check your model before… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling PDB File Format Explained: ATOM, HETATM and Every Column Learn to read a PDB file column by column, from altLocs to B-factors, and fix the five format faults that break docking… Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling TIP3P vs SPC/E vs TIP4P: Which Water Model in GROMACS? Pick the water model your force field was built with. See the pairing rule, real property data and the exact pdb2gmx and… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Vina Scoring Functions: Vina vs Vinardo vs AD4 (–scoring) Vina, Vinardo or AD4? Learn what the --scoring flag changes, the exact command for each, and how to test them by redocking.… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling gmx rdf Tutorial: Radial Distribution Function in GROMACS Calculate a radial distribution function with gmx rdf: water, ions and binding-site solvation, coordination numbers and fixes. Run it on your trajectory. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling iMODS Tutorial: Normal Mode Analysis Step by Step Run iMODS normal mode analysis on a protein or docked complex, read every plot correctly, and avoid the input traps. Follow the… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Template Selection for Homology Modelling: A Guide Learn to find and rank homology modelling templates with BLASTp, HHpred and SWISS-MODEL using identity, coverage, resolution and state. Start here. Dr. Abdul Rajjak Shaikh 11 min read Molecular Modeling Contact Map Analysis in GROMACS with gmx mdmat Build a residue contact map from a GROMACS trajectory with gmx mdmat, then a contact-frequency heatmap in MDAnalysis. Compare wild type and… Dr. Abdul Rajjak Shaikh 12 min read