When dealing with biomolecular systems, especially proteins, understanding the charge distribution of residues plays a critical role in many modeling tasks. Whether you’re preparing input for electrostatics calculations, identifying potential binding sites, or simply studying protein-ligand interactions, selecting residues based on their side chain charges helps focus your analysis and enhances accuracy.
In SAMSON, the integrative molecular design platform, you can leverage the Node Specification Language (NSL) to efficiently find and filter residues with specific properties — including their side chain charge.
Why charge matters 🔋
Charged residues — such as Aspartate (ASP), Glutamate (GLU), Lysine (LYS), Arginine (ARG), and Histidine (HIS) — play important roles in catalytic sites, salt bridges, and molecular interactions. Being able to isolate these charged amino acids helps with tasks like:
- Predicting protonation states
- Designing mutations
- Grouping residues for electrostatic potential calculations
Selecting residues with specific charges
You can use the residue.charge attribute in NSL to target residues based on their side chain charge:
r.c neg— matches negatively charged residues (e.g., ASP, GLU)r.c pos— matches positively charged residues (e.g., LYS, ARG)r.c neu— matches residues with neutral side chainsr.c un— matches residues with undefined charge
You can also combine values to target multiple types at once. Example:
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r.c neu, pos |
This matches all residues with neutral or positive side chain charges — helpful for isolating regions that are either uncharged or positively charged.
Practical examples
Here are a few use cases molecular modelers might find helpful:
Identify all positively charged residues
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node.type atom in r.c pos |
This retrieves the atoms of all positively charged residues, which you can use to examine electrostatic complementarity in binding sites.
Highlight both acidic and basic residues
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r.c neg, pos |
This selects residues that can form salt bridges or participate in pH-sensitive interactions.
Exclude undefined charges for clarity
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not r.c un |
This can be useful when preparing a cleaned-up model for electrostatics-based analysis.
Final thoughts
With SAMSON’s Node Specification Language, filtering residues by their side chain charge only takes a few characters — but it can significantly improve how you prepare your molecular systems. Whether you’re analyzing active sites, setting up calculations, or generating visuals, understanding and using residue.charge helps you get better control over your data and interpretation.
To learn more about how to use charge and other residue attributes in SAMSON, visit the full documentation page here:
https://documentation.samson-connect.net/users/latest/nsl/residue/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.