Tag
Structural Bioinformatics
Bioinformatics How to Predict Conformational B-Cell Epitopes Run ElliPro, DiscoTope 3.0 and SEPPA 3.0 on a structure, read their scores correctly, and avoid the residue-numbering trap. Ragini Mishra 17 min read Updated Molecular Modeling PyMOL Commands for Docking and MD: Beginner Cheat Sheet Learn the PyMOL commands docking and MD students use every week, from binding-site selections to polar contacts and ray-traced figures. Start here. Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling AlphaFold pLDDT and PAE Scores: Is Your Model Good Enough? Read pLDDT from the B-factor column and the PAE plot, then apply a clear go/no-go rule for docking or MD. Learn which… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling MODELLER Tutorial: Build a Homology Model Step by Step Install MODELLER, pick a template, write the align2d alignment, run AutoModel and rank your models by DOPE score, using the official tutorial… Dr. Abdul Rajjak Shaikh 16 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 Remove Water Molecules From a PDB File for Docking Strip HOH waters and crystallisation additives from a PDB file with PyMOL, ChimeraX or pdb-tools, and learn which structural waters to keep. Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Dock a Ligand to a GPCR or Membrane Protein with AutoDock Vina (Step by Step) Dock a ligand into a GPCR with AutoDock Vina: pick the right activation state, strip BRIL and T4 lysozyme, and place the… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Predict a Protein-Protein Complex with AlphaFold-Multimer in ColabFold (Step by Step) Learn how to model a protein-protein complex free in ColabFold, set the chain break correctly, and judge ipTM, pTM and PAE before… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling How to Dock a Peptide to a Protein (HPEPDOCK, HADDOCK and AutoDock CrankPep): A Step-by-Step Guide Learn peptide-protein docking step by step with HPEPDOCK, HADDOCK and AutoDock CrankPep, and find out which one to run for your project. Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Handle Metal Ions in Molecular Docking and MD (Zinc, Magnesium and Iron, Step by Step) Stop deleting the zinc. Learn when to keep a metal ion, how to dock into a metalloprotein with AutoDock4Zn, and how to… Dr. Abdul Rajjak Shaikh 15 min read