Tag
Drug Design
Molecular Modeling How to Write the Methods Section for a Molecular Docking Study Write a docking methods section a reviewer accepts. Get the reporting checklist plus a worked, copy-adaptable AutoDock Vina example. Dr. Abdul Rajjak Shaikh 10 min read Updated Drug Design 7 Molecular Docking Project Ideas for Your MSc Thesis (and Your CV) Pick a scoped, defensible molecular docking project you can finish with free tools and public data. Start building your thesis today. Dr. Abdul Rajjak Shaikh 7 min read Updated Molecular Modeling How to Set the Grid Box in AutoDock Vina: Center and Size Explained (Step-by-Step) Set the AutoDock Vina grid box the right way: find the binding-site center, pick a box size in Angstroms, and stop guessing… Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling How to Parameterize a Small-Molecule Ligand for a GROMACS Simulation: CGenFF vs ACPYPE vs ATB Learn how to build a GROMACS-ready ligand topology. Compare CGenFF, ACPYPE and ATB, then prepare a defensible protein-ligand system step by step. Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling Protein-Ligand MD Simulation in GROMACS: A Step-by-Step Tutorial for Beginners Turn a docked pose into a real protein-ligand trajectory in GROMACS. Build the ligand topology, solvate, equilibrate, and run. Start your MD… Dr. Abdul Rajjak Shaikh 12 min read Updated Career Guide 8 Molecular Dynamics Project Ideas for Your MSc Thesis (GROMACS) Eight scoped, finishable GROMACS molecular dynamics project ideas for an MSc thesis, each with a research question, deliverable, and difficulty. Pick yours… Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling How to Prepare a Protein and Ligand for Molecular Docking (Step-by-Step Beginner’s Guide) Learn how to prepare a protein and ligand for docking, clean the PDB, add hydrogens and charges, and export PDBQT files. Get… Dr. Abdul Rajjak Shaikh 10 min read Updated Bioinformatics Unveiling the World of Molecular Dynamics Simulation Courses Molecular dynamics (MD) simulation is a powerful computational technique that allows researchers to study the behavior of molecules and their interactions over… Dr. Abdul Rajjak Shaikh 3 min read Updated Bioinformatics Basics of Drug Designing Drug design is the process of using computational methods and technologies to identify and develop new drugs that can be used to… Dr. Abdul Rajjak Shaikh 2 min read Updated Molecular Modeling Why Protein Docking, Molecular Modeling and Simulation are essential skills to learn Protein docking, molecular modeling, and simulation are all essential techniques in the field of structural biology. These techniques allow scientists to understand… Dr. Abdul Rajjak Shaikh 2 min read Updated