Understanding and Using Residue Attributes in Molecular Design

Molecular modelers often face the challenge of efficiently analyzing and manipulating specific residues within complex molecular structures. SAMSON, the integrative molecular design platform, provides a powerful solution. With its Node Specification Language (NSL), SAMSON offers a structured system to define and query residue attributes, enabling users to work seamlessly with residues across a diverse range of contexts.

Why Residue Attributes Matter

Residue attributes in SAMSON allow users to define, query, and classify residues based on specific properties. By using residue attributes, you can identify key structural features, perform chemical analysis, or streamline large-scale simulations. Whether you’re isolating residues by charge, secondary structure, or chemical composition, SAMSON’s flexibility ensures high efficiency and precision.

Key Residue Attributes to Know

The residue attributes in SAMSON fall into different categories, offering a variety of functionalities. Here’s an overview:

1. Inherited Node Attributes

  • Visibility: r.v attributes (e.g., r.v, not r.v) help you determine whether a residue is visible or hidden in the molecular view.
  • Selection: The r.selected attribute distinguishes residues part of or excluded from current selections (not r.selected).
  • Names: Use r.n to query residues by their names. For instance, identify residues with a name starting with “L” using r.n "L*".

2. Structural and Chemical Properties

  • Charge: Identify negative, neutral, or positive residues via r.c neg, r.c neu, or r.c pos. This is particularly helpful for analyzing charge interactions in biomolecules.
  • Hydrophobicity: Use the hydrophobicity scale (Kyte & Doolittle, 1982) with r.hydrophobicity attributes to analyze regions with hydrophobic (negative) or hydrophilic characteristics. For example, define a range with r.hydrophobicity < 0.

3. Secondary Structure and Type

  • Secondary Structures: Query alpha helices, beta strands, or unstructured regions using r.ss alpha, r.ss beta, and similar short codes (r.ss h or r.ss b).
  • Types: Residues like alanine (r.t ALA) or lysine (r.t LYS) can be filtered by specific chemical types or amino acid categories.

4. Unique Residue Indicators

  • Terminal Status: Terminal residues can be identified with the r.ter attribute, helpful for pinpointing areas like molecular ends or chain termini.
  • Standard Name: Attributes like r.srn or r.nsrn enable users to distinguish between standard and non-standard PDB residue names.

How to Use These Attributes

SAMSON makes querying residue attributes straightforward. To match residues meeting multiple criteria, you can easily combine conditions. For instance:

  • r.v and r.c pos: Matches visible residues with positive charges.
  • r.ss h and r.ter: Focuses on residues part of alpha helices that are also terminal.

Combined queries empower sophisticated molecular designs, simplifying workflows for biochemists, structural biologists, and drug designers alike.

Conclusion

Residue attributes in SAMSON provide an essential toolkit for molecular design professionals. From detailed structural analysis to precise chemical selection, these features greatly enhance capabilities while reducing manual effort. For more details and practical examples, visit the official documentation page.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at this link.

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