Targeting Residues by Charge and Polarity in SAMSON

One common challenge in molecular modeling is efficiently locating specific types of residues based on their physicochemical properties. For example, you might want to highlight all positively charged residues in a protein to identify likely binding sites for negatively charged ligands, or filter for polar residues when studying interactions with water.

If you’re using SAMSON, the integrative molecular design platform, you can perform such tasks using the Node Specification Language (NSL). In this post, we’ll explore how to find and filter residues based on their charge and polarity, giving you greater control over your selection and analysis workflows.

Working with Residue Charges

Residues—particularly amino acids—can have side chains with different electrical charges. With NSL, you can use the residue.charge attribute (short version: r.c) to locate residues that are:

• negative (neg)
• neutral (neu)
• positive (pos)
• undefined (un)

For example:

This matches amino acid residues with a positive side chain charge. You can also combine multiple charges:

This query finds residues with neutral or positive side chains—great for isolating non-acidic regions of a protein.

Polarity as a Selection Filter

Polarity plays a critical role in determining how residues interact with their environment. For instance, hydrophobic residues tend to cluster in the core of a protein, whereas polar or charged residues are more often solvent-exposed. You can use residue.polarity (short version: r.p) to match the following types:

• acidicPolar (acidic)
• basicPolar (basic)
• nonpolar
• polar
• undefined (un)

Some examples:

This matches residues with a polar side chain (including acidic and basic ones).

This matches residues that are either acidic or basic.

Use Cases and Combinations

By combining charge and polarity selections, you can craft fine-tuned filters:

This matches basic residues with a positive charge—likely candidates for interacting with DNA or phosphorylated ligands.

This results in acidic residues with a negative charge. These might play roles in catalysis or metal binding.

Bonus: Hydrophobicity Filter

You can go even further by using the residue.hydrophobicity attribute (based on the Kyte-Doolittle scale) to select residues based on how hydrophobic or hydrophilic they are:

This selects residues that are hydrophilic, which might be important when identifying solvent-exposed regions.

Conclusion

Residue selection in NSL with SAMSON is more than just a visual aid—it can help you guide simulations, identify binding interfaces, or optimize molecular designs by providing precision access to molecular subsections.

To explore more attributes (like partial charges, residue types, and backbone completeness), check the full documentation: Residue attributes in SAMSON NSL.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.