Efficiently Filter Charged Residues in SAMSON with NSL

When working on protein modeling workflows, one of the recurring tasks is identifying and selecting residues based on their electrical charge. Whether you’re optimizing electrostatic interactions, analyzing salt bridges, or preparing electrostatics-related simulations, filtering charged amino acids is a crucial first step. In SAMSON, the Node Specification Language (NSL) provides a precise and easy way to achieve this.

This post introduces how to leverage the residue.charge attribute to filter residues by side chain charge using NSL — a useful tip to streamline your structural analysis and selection processes.

Why Focus on Side Chain Charges?

The side chain charge of a residue affects its behavior in molecular interactions like binding, solvation, or forming hydrogen bonds. Charged residues can help identify active sites, predict pKa shifts, or detect potential interaction hotspots. Common examples include:

  • Positively charged residues like LYS and ARG
  • Negatively charged residues like ASP and GLU
  • Neutral residues such as ASN or GLN

Using NSL to Filter by Charge

In SAMSON’s NSL, you can use residue.charge (short name: r.c) to select residues based on their side chain charge. Here are some handy examples:

  • r.c neg: Selects all residues with a negative side chain charge.
  • r.c pos: Selects positively charged residues.
  • r.c neu, pos: Selects residues that are either neutral or positive.

This is especially useful if you’re designing charged patches, tuning electrostatics in docking simulations, or filtering for electrostatic complementarity.

Combine with Atom-Level Queries

You can also combine this query with atom-level filters. For example:

This selects all atoms in residues with positive side chain charges.

Best Practices

  • Always double-check the secondary structure context — some charged residues play specific structural roles.
  • Use r.pI, r.pKa1, and r.pKa2 if you need more detailed electrostatic profiling.
  • Combine charge selection with r.ss (secondary structure) to find charged residues in helices or loops.

Filtering by charge via NSL in SAMSON helps you focus on the residues that may significantly impact molecular function, interaction, or stability.

To learn more, refer to the full documentation page here: NSL Residue Attributes Documentation.

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

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