When working on structure-based drug design or biomolecular modeling, it’s often necessary to filter or classify molecules based on the properties of their components. For example, identifying side chains with a particular number of carbon atoms, or selecting only those that contain nitrogen but no sulfur, might be critical in preparing a model for simulation or analysis.
The good news: if you’re using SAMSON, the Node Specification Language (NSL) provides rich filtering options to streamline this process, especially when dealing with side chain nodes.
Why focus on side chains?
Side chains often define much of the molecular behavior, influencing interactions, binding affinities, and solubility. For researchers building or analyzing proteins, ligands, or small molecules, classifying or targeting specific side chains is essential to ensure accuracy and efficiency, particularly when preparing systems for simulation or when interpreting structure-activity relationships.
Using NSL to filter side chains by atom count
NSL allows you to select side chains based on several structural attributes. These attributes can be used when crafting queries to find nodes that match specific criteria. Here are some of the most useful attributes when focusing on side chains:
- numberOfAtoms (nat) – total number of atoms in the side chain
- numberOfCarbons (nC) – number of carbon atoms
- numberOfHydrogens (nH), numberOfNitrogens (nN), numberOfOxygens (nO), numberOfSulfurs (nS): counts per element
- numberOfCoarseGrainedAtoms (ncga) – for multi-scale modeling
You can use these attributes in NSL with either value ranges or comparison operators. For instance:
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sc.nC > 5 |
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sc.nO 2:4 |
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sc.nat < 100 |
These expressions would match:
- Side chains with more than 5 carbon atoms
- Side chains with 2 to 4 oxygen atoms
- Side chains with fewer than 100 atoms total
Combining conditions
You can combine attributes using logical operators. For example, to select side chains with more than 10 total atoms and with at least one nitrogen but no sulfur:
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1 |
sc.nat > 10 and sc.nN > 0 and sc.nS 0 |
This type of search can help isolate chemically relevant side chains while omitting those unlikely to participate in desired interactions.
Visual inspection and selection
In SAMSON, after applying an NSL selection, the result can be highlighted directly within the molecular viewer. This not only speeds up model refinement but avoids manual errors in selecting desired components.
This strategy is particularly effective when preparing systems for quantum calculations, selecting fragments for docking, or identifying chemically reactive groups.
To explore all available side chain filtering options in NSL, including additional attributes like formal charge or partial charge, visit the side chain attribute documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.