Tag
Protein-Ligand Interactions
Molecular Modeling Discovery Studio Visualizer Tutorial: How to Analyse Docking Results and Make 2D Interaction Diagrams Load your docked pose, list every contact with its distance, and export the 2D interaction diagram your thesis needs. Follow the full… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling How to Analyze Protein-Ligand Interactions Over an MD Trajectory (ProLIF and MDAnalysis, Step by Step) Compute which binding-site residues held your ligand and for what percentage of the run, using ProLIF and MDAnalysis on a PBC-corrected GROMACS… Dr. Abdul Rajjak Shaikh 11 min read Updated Drug Design How to Make 2D Protein-Ligand Interaction Diagrams (LigPlot+ & PLIP): Step by Step Turn any AutoDock Vina or PyRx docking pose into a publication-ready 2D interaction diagram with free tools. Follow the LigPlot+ and PLIP… Dr. Abdul Rajjak Shaikh 9 min read Updated