When working on molecular modeling projects, searching for structural patterns within large biomolecules is often time-consuming. Whether you’re looking to identify highly charged side chains, filter out side chains with a large number of atoms, or isolate specific functional groups based on atom types, scouring a molecular structure manually is tedious.
Fortunately, SAMSON provides a powerful tool with its Node Specification Language (NSL), and the sideChain attribute space lets you express these queries concisely and effectively. Here’s how you can use it to make your workflow more efficient and accurate.
What is the Side Chain Attribute Space?
The sideChain attribute space (short name sc) in NSL provides access to properties specifically related to side chain nodes in molecular structures. This means you can filter based on atom counts (carbon, hydrogen, oxygen…), charges, and other molecular descriptors without writing long scripts or manually browsing molecules.
Useful Filters You Can Use Immediately
Let’s say you want to find all side chains with:
- More than 1 unit of formal charge:
sc.fc > 1 - Between 10 and 20 carbon atoms:
sc.nC 10:20 - Fewer than 100 atoms total:
sc.nat < 100 - Partial charge above 1.5:
sc.pc > 1.5
This makes it easier to locate highly functionalized regions, determine candidate side chains for modification, or analyze the structure’s biophysical behavior in a rational way.
Why Does This Matter?
Imagine you’re refining a drug-like molecule and want to limit your design to side chains that are relatively small, neutral, and hydrophobic. Rather than browsing manually, you can use queries like:
|
1 |
sc.fc 0 and sc.nO < 2 and sc.nN < 2 and sc.nat < 30 |
Or, if you’re performing charge distribution analysis and need to find charged groups:
|
1 |
sc.fc > 0 or sc.pc > 1.0 |
These queries help you prototype faster, communicate better with colleagues, and integrate searches into automated workflows.
Quick Reference for Atom Counters
| Property | Short name | Example |
|---|---|---|
| Number of atoms | nat |
sc.nat 100:300 |
| Number of carbons | nC |
sc.nC > 10 |
| Number of hydrogens | nH |
sc.nH < 5 |
| Number of nitrogens | nN |
sc.nN 1 |
| Number of oxygens | nO |
sc.nO 2:4 |
| Number of sulfurs | nS |
sc.nS > 0 |
| Coarse-grained atoms | ncga |
sc.ncga < 100 |
Try It On Your Projects
Whether you’re working with complex proteins, small molecules, or hybrid systems, try using these attribute filters directly in your SAMSON search bar or in scripts. Tweak ranges, combine multiple filters, and save time identifying exactly what you’re looking for in seconds.
To learn more about attribute-based filtering in the sideChain space, visit the official SAMSON NSL Side Chain Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.