Tag
Structural Bioinformatics
Bioinformatics I-TASSER Tutorial: Predict Structure and Read the C-score Submit a sequence to the free I-TASSER server, pick the right one of five models, and read C-score, TM-score and RMSD correctly.… Dr. Abdul Rajjak Shaikh 12 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 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