video1.0<iframe src="https://www.loom.com/embed/96152485df7a4179b2a4e946f92294ea" frameborder="0" width="1920" height="1440" webkitallowfullscreen mozallowfullscreen allowfullscreen></iframe>14401920Loomhttps://www.loom.com14401920https://cdn.loom.com/sessions/thumbnails/96152485df7a4179b2a4e946f92294ea-f006d5a1857eeb78.gif304.064In this video, I walk you through the process of ensemble docking, starting with running a protein in water molecular dynamics simulation. I explain how to set up your simulation, including naming it, uploading PDB files, and adjusting force fields and simulation time. After running the simulation, I guide you on how to preprocess the MD data and set up the docking algorithm to analyze the protein's dynamic interactions with compounds. I emphasize the importance of aligning the docking box with the protein's pocket and collecting data across multiple snapshots. Please make sure to follow the steps carefully and prepare your CSV files for data engineering.