A binding site can look inaccessible in a static structure even when a protein’s flexibility may create room for a ligand. The challenge is exploring that motion without manually dragging atoms or mistaking a single snapshot for the whole story. Nonlinear normal modes offer a way to investigate large-scale structural movements—such as pocket opening and closing—interactively in SAMSON.
This workflow uses the Normal Modes Advanced extension, which computes nonlinear normal modes with the NOLB algorithm. It is designed for biomolecular systems including proteins, RNA, and DNA. The steps below focus on a practical question: how might a structure move toward an open binding site, and how can you keep useful conformations for later analysis?
Start with a structure and a focused calculation
Open a biomolecular structure in SAMSON. The tutorial uses the protein structure 1VPK, but you can use another suitable model. Before calculating, decide whether you want to explore the whole structure or focus on a region. If you select residues first, the calculation can be performed on that subset; otherwise, it can use the full structure.
In the Normal Modes Advanced module, choose the number of modes, the interaction cutoff distance, and the potential function. The interface currently provides the elastic network model potential. These choices affect what motion you will inspect, so a useful approach is to begin with a manageable calculation and explore the resulting modes before refining your setup.
Explore modes without losing the bigger picture
Once the calculation finishes, each mode has a slider that lets you inspect its motion. Move a slider to see how the structure changes. A mode can be checked and combined with other checked modes; use play to apply the selected motions as a trajectory. You can also adjust unchecked sliders while motion is playing, which makes it possible to explore combinations interactively.
For a binding-site question, keep your attention on the residues that define the pocket and the surrounding structure. Does the opening you are looking for appear in one mode, or does it require a combination? Does changing the motion amplitude reveal a useful movement, or simply make the structure harder to interpret? These are practical exploration questions—not evidence that a particular conformation is experimentally populated.
You can change the transformation between linear motion (translations only) and nonlinear motion (translations and rotations), and adjust the scaling factor to change motion amplitude. Motion speed and harmonic behavior can also be changed. Forward and backward step controls let you inspect the trajectory incrementally rather than relying only on continuous playback. If you activate real-time minimization, the module provides three minimization algorithms to choose from.
Define the target you want to approach
When visual browsing is not specific enough, use the Structure Definition tab. A target structure can be defined using residues or atoms, and the module can search for a combination of modes that reaches that target. This gives the exploration a concrete objective—for example, a desired pocket arrangement—instead of asking you to judge every motion by eye.
As you compare candidate motions, keep track of what was changed: which modes were checked, their slider values, the scaling factor, and the motion type. These settings matter when saving a trajectory, because the saved result uses the current calculation settings. Recording them alongside your observations can make later comparisons easier.
Save a useful state, not just a moving preview
When you find a conformation worth revisiting, press S to store it as a SAMSON conformation. This is convenient for restoring a state in the document. If you need to superpose multiple structural states, create a SAMSON structural model instead; you can select the whole structure or just part of it. The current structure can also be exported as a PDB file.
To preserve a sequence of motion, configure the saving interval in the Save frames tab. You can store frames as conformations or export them as PDB files. Alternatively, use the Path button to store the trajectory in a SAMSON trajectory node. This turns an exploratory session into something you can revisit, compare, and carry into subsequent analysis.
The key benefit is a more structured way to investigate flexibility: calculate modes, test combinations against a pocket-opening objective, inspect the motion at different scales, and save states that are useful for the next step. For the complete walkthrough, see the Normal Modes Advanced tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.