HeyJaredScience with AI - Analysis to Writing
Welcome to Science with AI - Analysis to Writing. This channel is your comprehensive guide to mastering the modern scientific workflow, from initial data discovery to final publication. We explore how Artificial Intelligence is revolutionizing every step of the research process.
- Indexed videos, last 90 days
- 8
- Latest publication
- Aug 27, 2026
- Audience
- ~188 subscribers
- Earliest in this view
- Aug 11, 2026
Latest videos
Automated GROMACS MD Pipeline | Native Protein & Protein–Ligand Simulations and Analysis (opens the original)
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Run complete molecular dynamics simulations through an automated, modular GROMACS workflow. The GRO MD Pipeline v25-03-2026, developed by Dr M Fayyaz ur Rehman, supports both native-protein and protein–ligand complex simulations. It checks the molecular structure, prepares the system, generates topology files, performs solvation and ionization, runs energy minimization, completes NVT and NPT equilibration, and executes configurable production MD simulations. The pipeline can resume interrupted s
Protein ligand Analysis using PLIP and PyMol. MD simaultions using GROMACS. Lysozyme in water (opens the original)
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Protein–Ligand Analysis Using PLIP and PyMOL | GROMACS MD Simulation of Lysozyme in Water Learn protein–ligand interaction analysis, protein preparation, solvation, ion addition, energy minimization, NVT and NPT equilibration using GROMACS. PLIP AND PYMOL pip install plip plip -f complex.pdb -o plip_results -xty pymol plip_results/*.pse LYSOZYME MD SIMULATION 1. Download protein: wget https://files.rcsb.org/download/1AKI.pdb 2. Remove water molecules: sed '/HOH/d' 1AKI.pdb | tee 1AKI_clean.pdb 3
Using AGFR, Autodock Vina and Virtual Screening (opens the original)
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Learn how to install the ADFR Suite on Ubuntu, define an accurate molecular-docking search box through the AGFR graphical interface, perform ligand–protein docking with AutoDock Vina, and extend the workflow to virtual screening. This practical session covers the complete workflow: • Downloading and installing ADFR Suite on Ubuntu • Launching the AGFR graphical user interface • Loading prepared receptor and reference-ligand PDBQT files • Locating the protein-binding pocket • Defining the grid-bo
Ligand Protein docking and analysing results using autodock tools (opens the original)
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In this hands-on tutorial, we perform ligand–protein molecular docking and analyse the docking results using AutoDockTools. The session explains the complete process—from loading prepared ligand and receptor PDBQT files to defining the grid box, running docking calculations, selecting the best binding pose and examining ligand–protein interactions. Topics covered: • Loading ligand and receptor PDBQT files • Identifying the protein-binding pocket • Defining the grid-box centre and dimensions • Pr
Preparing files for docking - github, openbabel and manual preparation by autodocktools (opens the original)
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Learn how to prepare ligand and protein files for molecular docking using both command-line and graphical tools. This practical tutorial covers the complete file-preparation workflow required before running docking experiments with AutoDock or AutoDock Vina. In this video, you will learn how to: • Download protein structures from the Protein Data Bank using wget • Access preparation scripts and supporting files from GitHub • Inspect and clean protein structures using PyMOL • Remove unnecessary w
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~188 subscribers
Measured Sep 19, 2026
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