Finding Charged Amino Acids in Large Systems: A Simple and Powerful Filter

When exploring large biomolecular structures in molecular modeling, one of the frequent needs is identifying specific residues by their chemical properties. Whether refining a force field, preparing an input file, or designing a mutation experiment, knowing exactly where the positively or negatively charged amino acid residues are located can be essential 🧬.

Thankfully, SAMSON’s Node Specification Language (NSL) offers a straightforward way to filter residues based on their side-chain charge. The residue.charge attribute (short name: r.c) allows you to match residues classified as negative, neutral, positive, or undefined, which is especially helpful when dealing with large proteins or nucleic acid-protein complexes.

Why this matters

Electrostatic interactions in biomolecular systems are not only critical for structural stability but also for function: binding affinity, solvation properties, and pKa shifts all tie back to charge. Manually identifying these residues—especially in large models—can be tedious and error-prone.

With NSL in SAMSON, you can retrieve exactly what you need with a minimal expression.

Quick syntax overview

Here’s how you can easily select these residues:

• r.c neg: Matches residues with a negative side-chain charge (e.g., ASP, GLU)
• r.c pos: Matches residues with a positive side-chain charge (e.g., LYS, ARG)
• r.c neu: Matches residues with a neutral side-chain charge (e.g., LEU, GLN)
• r.c un: Matches residues with undefined side-chain charge (e.g., unknown or modified residues)

You can also combine filters using commas:

This expression matches residues that are either negatively or positively charged—essentially highlighting all charged amino acids.

Targeting specific residue atoms

If you want to specify atoms within those charged residues, that’s also possible. For instance, to select the alpha carbon (CA) atoms within positively charged residues, you could use:

Integration with other filters

You can combine residue.charge with other attributes like secondary structure or residue name. For example, to find positively charged residues in alpha helices:

Useful tip: Visual inspection and coloring

Using NSL filters in SAMSON isn’t just about selection—you can quickly color or isolate these residues, aiding in visual analyses or export for simulations. For instance, color all negatively charged residues red and positive ones blue before exporting an image or saving a filtered structure. It speeds up communication and presentation.

Practical example: Identify and mutate

Need to test how replacing negatively charged residues affects protein stability? Use:

Then, you can quickly apply mutation tools or assign custom properties only to these residues.

To learn more and explore other residue attributes (like polarity, type, and secondary structure), visit the full documentation: 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.