If you’ve ever worked with biomolecular structures, you’ve likely faced the challenge of identifying specific types of residues—such as acidic side chains, positively charged amino acids, or those with specific pKa ranges. These tasks are essential for setting up simulations, modifying protonation states, visualizing electrostatic potentials, or simply understanding molecular interactions.
In SAMSON, the integrative molecular design platform, the Node Specification Language (NSL) provides a compressed and readable syntax to filter, search, and select residues based on a wide variety of attributes. In this post, we focus on attributes that relate to residue charge, polarity, and pKa—three properties often needed for tasks like environment-dependent modeling, pH adjustments, or evaluating solubility and interaction sites.
Target residues by charge
The residue.charge attribute (short version: r.c) allows you to select residues based on their side chain charge. You can match:
r.c neg– residues with negative side chain charger.c pos– residues with positive side chain charger.c neu– residues with neutral side chain charger.c neg, pos– exclude neutral residues
This is particularly useful in salt bridge detection or to verify charged patches across the surface of a protein.
Refine your search with polarity
Beyond charge, polarity gives another layer of chemical behavior. The residue.polarity attribute (short version: r.p) provides access to polarity types, such as:
r.p acidic– acidic polar residues like Asp or Glur.p basic– basic polar residues like Lys or Argr.p nonpolar– hydrophobic residuesr.p polar– non-charged polar residues
This can help classify binding interfaces, or assess hydrophobic pockets in proteins or protein-protein interfaces.
Target specific pKa or isoelectric point ranges
If you’re looking to analyze residues that protonate or deprotonate at certain pH levels, three properties come in handy:
r.pKa1– pKa of carboxyl groups (typically lowers, like Asp)r.pKa2– pKa of amino groups (like Lys, Arg)r.pI– isoelectric point of the entire residue
Some example NSL queries:
|
1 2 3 |
r.pKa1 < 2.0 # Carboxylic residues with low pKa r.pKa2 7.5:9.0 # Amino groups in slightly basic range r.pI < 6.0 # Residues with low isoelectric point |
These are useful during pKa calculations, protein titration state assignments, or making educated guesses about residues to mutate for pH-sensitive designs.
Why this helps
Using these attributes, you can create highly specific filters in seconds. For example:
|
1 2 |
n.t a in r.c neg and r.p acidic # atoms in acidic, negatively charged residues n.t a in r.pKa2 > 9.0 # atoms in residues with high amino group pKa |
No need to manually scroll through lists or highlight residues by hand. Combine attributes to identify unique subsets, like basic residues with pI above 9 or polar residues with a non-standard residue name.
These features aren’t just useful for large-scale data extraction—they’re great even when working on a single chain or subunit, helping speed up visualization and insight generation. 🎯
For more information, including the full list of supported attributes (from visibility flags to hydrophobicity), visit the original NSL documentation page: https://documentation.samson-connect.net/users/latest/nsl/residue/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.