Tag
Structural Bioinformatics
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 Molecular Modeling How to Set Protonation States and Add Hydrogens to a Protein Before Docking or MD (PDB2PQR, PROPKA and H++) Crystal structures ship without hydrogens. Learn to predict pKa values with PROPKA, protonate with PDB2PQR or H++, and check the result before… Dr. Abdul Rajjak Shaikh 14 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 UCSF ChimeraX Tutorial for Beginners: Load, Inspect and Clean a Protein Structure Learn UCSF ChimeraX in one sitting: fetch a PDB entry, master the 12 core commands, then clean the structure for docking or… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Predict the Effect of a Mutation on Protein Stability (DynaMut2, mCSM and DDMut): A Step-by-Step Guide Predict how a point mutation changes protein stability with DynaMut2, mCSM and DDMut, and learn to read the ddG sign correctly before… Dr. Abdul Rajjak Shaikh 17 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 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 Align and Superimpose Two Protein Structures in PyMOL (align, super and cealign): A Step-by-Step Guide Learn to superimpose two proteins in PyMOL with align, super and cealign, read the RMSD, pick the right command, and fix zero-atom… Dr. Abdul Rajjak Shaikh 10 min read Updated