Quick Guide: How to Use the Base TMDD Module

Learn how to use the base TMDD module with this step-by-step guide. Discover how to load the single TMDD module, rename molecules, and run simulations efficiently.

December 11, 2025 By Wilbert de Witte

In this guide, we'll learn how to use the base TMDD module to set up a simulation. We will cover how to load the module, rename molecules to match your base PKSim module, and remove unnecessary building blocks. By following these steps, you will prepare your simulation for accurate results.

Let's get started

Here’s a quick guide on how to use the base TMDD module. First, we load the module.

Step #1: Right-click on "Modules" — Right-click on "Modules"

Step #2: Click on "Load Module" — Click on "Load Module"

Step #3: Click here — Click here

It's called single TMDD. It has two building blocks: one for molecules and one for reactions.

Step #4: Click on "Open" — Click on "Open"

For the molecules, it says to remove them after renaming.

Step #5: Click here — Click here

We need to rename these molecules and give them the same names as in our base PKSim module.

Step #6: Double-click on "Y Molecules -REMOVE AFTER RENAMING-" — Double-click on "Y Molecules -REMOVE AFTER RENAMING-"

Step #7: Click here — Click here

What we do here is...

Step #8: Right-click on "- Target Complex - RENAME" — Right-click on "- Target Complex - RENAME"

We rename the drug target complex.

Step #9: Click on "Rename" — Click on "Rename"

To the name of the drug target complex in the base module.

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Type the name of your drug-target complex, in this example "ADC-TMEFF2-Boswell et al."

Step #11: Click on "OK" — Click on "OK"

Okay.

Step #12: Click here — Click here

Next, rename the target.

Step #13: Right-click on "Target -RENAME-" — Right-click on "Target -RENAME-"

Step #14: Click on "Rename" — Click on "Rename"

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Type "TMEFF2"

Step #16: Click on "OK" — Click on "OK"

Step #17: Click on "OK" — Click on "OK"

We are almost finished. Now, we just need to remove the entire molecule's building block.

Step #18: Right-click on "Molecules -REMOVE AFTER RENAMING-" — Right-click on "Molecules -REMOVE AFTER RENAMING-"

Step #19: Click here — Click here

I delete this one, then we build a new simulation.

Step #20: Click on "Yes" — Click on "Yes"

Add our TMDD module to the base module.

Step #21: Right-click on "Simulations" — Right-click on "Simulations"

Step #22: Click on "Create Simulation ..." — Click on "Create Simulation ..."

Step #23: add the base module — add the base module

Step #24: Add "Single target and complex turnover" — Add "Single target and complex turnover"

Step #25: Click on "Configure" — Click on "Configure"

We need the target expression profile and should give the simulation a name.

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add the expression profile

Step #27: Type a name — Type a name

Step #28: Click on "OK" — Click on "OK"

Step #29: Click on "Results" — Click on "Results"

Now we can run the simulation and finish.

Step #30: Click on "Run Define Settings Configure Stop all running" — Click on "Run Define Settings Configure Stop all running"

Quick Guide: How to Use the Base TMDD Module