Efficiently Target Residues in Molecular Models with Smart Tagging

When working with complex biomolecular structures, one of the most common tasks is selecting specific residues based on properties like charge, polarity, backbone completeness, or location within the secondary structure. This need arises in countless scenarios: analyzing binding pockets, preparing sites for mutation, cleaning structures for simulations, or filtering out non-standard residues.

Manually locating these residues in large datasets can be time-consuming — and error-prone. That’s where SAMSON’s Node Specification Language (NSL) comes in. NSL enables powerful, human-readable selection expressions to refine and target residues using precise attributes.

Why residue selection matters

Imagine you’re modeling protein-ligand interactions and need to:

• Find all positively charged residues near the binding site
• Exclude non-standard amino acids from your system
• Identify terminal residues for chain capping
• Inspect only residues forming alpha helices or beta strands

Rather than clicking through a structure manually, you can run a concise query. This streamlines workflows and reduces human error.

Practical examples of residue selection

SAMSON’s NSL for residues includes intuitive attributes with both long and short syntaxes. Here’s how you might use them:

Select by charge

To isolate residues based on side chain charge:

This targets all positively charged residues. You can combine multiple values like this:

Select by secondary structure

Sometimes you want to observe helices or beta sheets:

Find terminal residues

You can get even more specific, for example, selecting alpha carbons in terminal residues:

Filter by residue type

To isolate histidines or a group of residues like VAL, LYS, and PRO:

Target residues by standard naming

Filter out ligands or modified residues using:

Layering conditions

You can combine attributes for highly specific selection. For instance, to find standard lysines in beta strands:

When residue structure matters

Need to distinguish between residues with complete and incomplete backbone atoms? Try:

This helps verify structural integrity before running calculations or simulations.

Residue sequence ranges

To isolate a range of residues by sequence number:

Or more complex selections:

With these filters, you can build precise queries for your molecular modeling tasks in SAMSON, saving time and bringing clarity to your structural explorations.

To learn more about all available attributes and how to combine them, visit the Residue Attributes Documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.