Understanding and comparing protein sequences in a structurally meaningful way is a central task for molecular modelers, especially when evaluating mutations, domain boundaries, or designing molecular variants. Yet, traditional sequence visualization tools are frequently disconnected from 3D molecular viewers, forcing researchers to switch between applications or manually cross-reference residue numbers.
This common workflow bottleneck is streamlined in SAMSON with the Sequence View: an integrated tool that allows users to explore molecular sequences directly from within the 3D environment.
What is the Sequence View?
The Sequence View in SAMSON is a side panel that displays the sequence of molecular structures, such as proteins and nucleotides, alongside structural selections and properties. This integration between sequence and structure makes it easier to interact with, select, and analyze parts of a molecule with precision and speed—without leaving the modeling window.
Why it Matters
Let’s consider a few common pain points it addresses for researchers and educators:
- Residue navigation: Jump directly to regions you want to explore in 3D, such as active sites or binding pockets.
- Structural comparison: Visually track sequence differences in homologous structures loaded side-by-side in SAMSON.
- Mutation analysis: Scroll through the sequence to identify and assess mutations or engineered variants.
- Improved teaching tools: Highlighting sequences and structures simultaneously eases learning for students new to structural biology.
How It Works
The Sequence View provides a color-coded, linear representation of chains and their residues. Users can click on residues or sequence regions to:
- Automatically highlight the corresponding atoms in the 3D view.
- Select specific residues using tools like the Node Specification Language (NSL).
- Apply materials, color palettes, or visual presets to customize how parts of the molecule appear.
This tight coupling between 1D and 3D representations helps modelers stay focused and reduces time spent coordinating selections.
Working with Multiple Chains
For structures with multiple chains, the Sequence View differentiates them clearly. Each chain can be collapsed or expanded for better overview, and you can isolate or highlight specific chains in the 3D view. This is useful for fragment-based design or analyzing protein complexes one chain at a time.
Integrating with Other Tools in SAMSON
The Sequence View works seamlessly with:
- The Interaction Designer for investigating inter-chain dynamics.
- Visual presets to quickly toggle visualization styles across selected residues.
- Default color palettes to mark functional sites or domains by category.
With all this in one place, SAMSON helps researchers make faster and more informed decisions during molecular design and analysis.
To learn more about SAMSON’s Sequence View and other features, visit the complete documentation page here: https://documentation.samson-connect.net/users/latest/references/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.