When working with complex biomolecular systems, understanding the structure of proteins at the residue and chain level is often essential. Whether you’re analyzing experimental data or designing molecular systems, pinpointing features such as conserved regions, mutation sites, or accessible residues usually involves switching between sequence data and structural visualization tools.
This context-switching can be time-consuming and error-prone—especially with large molecular assemblies. In SAMSON, an integrative platform for molecular modeling and design, the Sequence View addresses this challenge directly by linking your sequence and structure data in an intuitive, visual, and fully interactive way.
Here’s how it can make your workflow simpler and faster.
Linked Selection Across Views
The Sequence View in SAMSON is tightly coupled with the rest of your working environment. When you select residues in the Sequence View, they are automatically selected in both the Document View and the 3D Viewport:
This real-time synchronization goes in both directions. Select a residue in the 3D Viewport, and it gets highlighted in the Sequence View. This drastically reduces the time needed to map sequence-based insight to 3D features—and helps improve accuracy in selecting the right segments for further operations, such as mutation, constraint definition, or simulation setup.
Exploring Biophysical Properties Visually
One of the key benefits of the Sequence View is the ability to color residues based on various biophysical properties. This is more than just decoration: color schemes can reveal hidden patterns, such as clustering of hydrophobic residues or charged zones near active sites. The visual encoding of property values makes it easier to interpret key sequence regions without needing to scroll through plain text data.
This color coding is not restricted to the 1D sequence: it is instantly reflected in the 3D structure as well, helping you gain immediate structural insight based on sequence characteristics. Whether you’re evaluating solvent exposure, hydrophobicity, or other parameters, the synchronized coloring provides consistent, informative views across representations.
Accessing Sequence Views
You can open the Sequence View through multiple paths, making it convenient whether you’re working through menus or contextual actions. From the Home menu, choose View sequence:
Alternatively, right-click on a model in your Document View and select Structural model > View sequence:
Handling Multi-Chain Structures
If a given structure contains several chains, a dialog lets you choose which sequences to visualize. This is especially useful when you’re working with multi-chain proteins, protein-DNA complexes, or viral capsids composed of repeating units:
This ensures you can focus on the most relevant parts of the biomolecular assembly—without being overwhelmed by unnecessary details.
Integrated Molecular Design Advantage
By bridging sequence and structure in a single, responsive interface, SAMSON’s Sequence View helps you save time and reduce errors in molecular modeling tasks. It is especially helpful for:
- Mapping experimental mutation data to models
- Identifying domains in complex proteins
- Preparing specific residue selections for simulations
- Understanding structure-function relationships
Want to dive deeper? Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.