Tag
Molecular Docking
Molecular Modeling How to Fix Missing Residues and Loops in a PDB Structure Before Docking or MD (ChimeraX, SWISS-MODEL and MODELLER) Find the gaps your crystal structure never resolved, decide which ones matter, and rebuild them in ChimeraX, SWISS-MODEL or MODELLER before docking… Dr. Abdul Rajjak Shaikh 15 min read Bioinformatics How to Dock a Multi-Epitope Vaccine Construct with TLR4: ClusPro, HDOCK and HADDOCK Compared Dock a screened vaccine construct against TLR4 the way a reviewer reads it: pick the PDB entry, prep the files, compare three… Ragini Mishra 16 min read Molecular Modeling How to Do Flexible Docking in AutoDock Vina (Flexible Side Chains, Step by Step) Learn how to let binding-site side chains move in AutoDock Vina: split the receptor with Meeko, run vina --flex, and judge whether… Dr. Abdul Rajjak Shaikh 14 min read Updated Molecular Modeling How to Dock Multiple Ligands in AutoDock Vina (Batch Docking): A Step-by-Step Guide Stop running Vina once per compound. Learn the --batch flag, the Open Babel prep loop, and how to pull 40 output files… Dr. Abdul Rajjak Shaikh 17 min read Updated Drug Design How to Check Drug-Likeness and ADMET of Your Docked Ligands (SwissADME, pkCSM and Lipinski’s Rule of Five) Learn to run SwissADME and pkCSM on your top docking hits, read the BOILED-Egg, and report Lipinski violations correctly in your thesis. Dr. Abdul Rajjak Shaikh 12 min read Updated 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 Molecular Modeling How to Find a Protein’s Binding Site for Docking with fpocket, CASTp and PrankWeb Predict a protein's binding pocket with PrankWeb, fpocket or CASTp, then convert it into the grid box coordinates AutoDock Vina needs. Dr. Abdul Rajjak Shaikh 15 min read Updated Bioinformatics How to Download a Protein Structure from the RCSB PDB and Read the File Find, download, and actually read a protein structure from the RCSB PDB before you dock or run MD. Start your modelling workflow… Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling How to Convert Molecular File Formats with Open Babel (PDB to PDBQT, MOL2 and SDF): A Beginner’s Guide Learn to convert PDB to PDBQT, MOL2, SDF and SMILES with Open Babel and get your docking files ready today. Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling Molecular Docking vs Molecular Dynamics: What’s the Difference, and Do You Need Both? Compare molecular docking and molecular dynamics: what a pose proves, what a trajectory adds, and why a defensible thesis project runs both… Dr. Abdul Rajjak Shaikh 11 min read Updated