Selecting the correct receptor is a foundational step in setting up a reliable docking simulation. Whether you are running a non-covalent or covalent docking study, errors made during this stage can severely impact your results. Yet, this step is often rushed or done based on assumptions about default settings.
This blog post shows how you can correctly define a receptor using the FITTED Suite in the SAMSON Molecular Design Platform, and highlights a few common mistakes to avoid.
Why the Setup of the Receptor Matters
The receptor is the macromolecular structure into which your ligand will dock. Defining it correctly ensures that the docking software recognizes the appropriate atoms, prepares the environment correctly, and considers critical molecular features like water molecules, metal ions, or flexible side chains.
Step-by-Step: Defining a Receptor with FITTED Suite
After launching SAMSON and loading your molecular structure (such as 1E2K.sam or 5MAJ.sam), the FITTED Suite helps streamline the receptor setup. Here’s how you do it:
- Select the protein structure in the Document view. This might be labeled something like
1E2Kor5MAJ, depending on your system. - In the FITTED Suite interface, navigate to the Set receptor section.
- Select From document and then click Set. This prompts FITTED to use your selected model as the receptor.
- Keep the Water molecules and Macromolecules fields to their default settings unless you’re working with non-standard systems like metalloproteins, DNA, or RNA. In those cases, adjust the Macromolecules parameter accordingly.
Tips to Avoid Common Mistakes
- Don’t forget to select the correct structural model in the document. If the file contains more than one model, make sure you target the specific one relevant to your docking study.
- Check for water molecules and alternate locations in the structure. Even though PREPARE helps with water molecules, in some complex systems, manual cleanup may still be necessary.
- Adjust macromolecule types wisely. For nucleic acids or metalloproteins, setting the right macromolecule class helps FITTED treat them with the correct docking assumptions.
What’s Next?
Once your receptor is set, you’ll need to define the binding site and ligand, and then proceed to docking. But if this initial receptor setup is done correctly, you’re building on a strong foundation.
This post is part of a larger tutorial available here:
Learn more about the FITTED Suite and integrative docking in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.