Tag
Molecular Modeling
Molecular Modeling How to Refine a Homology Model That Failed Validation Your model failed MolProbity or SAVES. Learn which refinement servers are live today, run ModRefiner step by step, and prove the fix… Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling PyMOL vs VMD vs ChimeraX: Which Should You Learn? Pick your molecular visualization tool by the job it does. Compare PyMOL, VMD and ChimeraX on licence, platforms and scripting before you… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Wild-Type vs Mutant MD Simulation in GROMACS Design a wild-type versus mutant MD comparison in GROMACS that survives examination: matched protocol, replicas, and a difference you can defend. Dr. Abdul Rajjak Shaikh 16 min read Molecular Modeling How to Run an MD Simulation of DNA or RNA in GROMACS Learn exactly what changes when you simulate a nucleic acid instead of a protein in GROMACS: force field, ions, box and analysis. Dr. Abdul Rajjak Shaikh 17 min read Updated Molecular Modeling How Many Replicate MD Simulations Should You Run? Learn why one trajectory is not enough, how many replicas an MSc project needs, and how to run and report them in… Dr. Abdul Rajjak Shaikh 11 min read Molecular Modeling ESMFold Tutorial: Predict Protein Structure in Seconds Fold a protein sequence with ESMFold in one curl command, read its pLDDT scores correctly, and learn when to use AlphaFold instead. Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Per-Residue Energy Decomposition with gmx_MMPBSA Turn one MM-GBSA number into a per-residue breakdown. Set up the decomp namelist, read the output and name your hotspot residues with… Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling How to Run GROMACS on an HPC Cluster with SLURM: Job Scripts, Modules and Restarts Move your GROMACS run from a laptop to a shared cluster. Load the right module, write a correct sbatch script, and restart… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Install PyMOL for Free (Open-Source PyMOL on Windows, Linux and Mac): A Step-by-Step Guide for Students Open-source PyMOL is free under a BSD-like licence. Install it with one conda command on Windows, Linux or Mac, then verify it… Dr. Abdul Rajjak Shaikh 13 min read Bioinformatics How to Get the Right Protein Sequence from UniProt for Modelling (Canonical Isoform, Signal Peptide and Residue Numbering) Pick a reviewed Swiss-Prot entry, take the canonical isoform, cut the signal peptide, and check the PDB offset before you model. Follow… Dr. Abdul Rajjak Shaikh 13 min read