Digital edition
Ebook · US$7.99
Learn with the book and its companion practice files when available.
Ordering opens after the book launch in December 2026.
A step-by-step practical guide · By Oluwatosin Saibu
Beyond the Pose
A step-by-step practical guide to molecular docking and molecular dynamics. Learn to prepare proteins and ligands, perform docking, evaluate binding poses, set up and run molecular dynamics simulations, and analyze your results through guided exercises.
Launching in December 2026. Get ready to learn molecular docking and molecular dynamics, step by step. Ordering, the first-chapter PDF and companion downloads will open after the book launch.
Learn the workflow. Understand the science.
Beyond the Pose
An introduction to computational chemistry through molecular docking and molecular dynamics.
Follow clear explanations, practical exercises and molecular illustrations from your first structure to the interpretation of a simulation. Work at your own pace with the companion files.
By Oluwatosin SaibuAbout 150 pagesCompanion files · Coming soon
US$7.99 ebook
Look inside ↓The first-chapter PDF will be available after the December 2026 book launch.
Hard copy · US$15.99
Prefer a printed book? The paperback edition is planned for the December 2026 launch. Shipping details will be announced when ordering opens.
Look inside
A taste of how you will learn
Explore concepts, illustrations and exercises from the opening chapter.
The first-chapter PDF will be available after the December 2026 book launch.
Your workflow, one step at a time
01 / Explore the structures
Download 181L, 187L, 6W63 and 7BQY, with a guide identifying each input and its source.
02 / Prepare and dock
Receptor and ligand preparation files, Vina configuration, fixed-seed docking log, selected pose and corrected redocking metric for 181L benzene.
03 / Simulate and analyze
The complete 100 ps teaching trajectory, matching TPR, energy files, AMBER/GAFF2 build records, MDP files and scripts for reproducing the analysis figures.
Start with README.txt inside the ZIP. You can analyze the supplied trajectory without rerunning MD.
Before you start
Keep a separate working folder for each exercise. Preserve the original inputs and record the versions of the tools you use. The starter structures require preparation before docking or molecular dynamics.
For software installers, use the official project websites: , AutoDock Vina and GROMACS. The main worked route uses command-line Vina, AmberTools and GROMACS; PyRx is optional. Follow the environment setup in the companion README.
Optional PyRx route
A graphical docking walkthrough for the same 181L–benzene example, with input files and a tested benzene pose-conversion helper. Use the main companion package for subsequent MD steps. Native installation depends on your operating system; see the included guide.
Contributors
Keep the companion close
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oluwatosinsaibu.com/beyond-the-pose/
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