A binding pocket can look inaccessible in a single structure, even when the protein may adopt other conformations. The challenge is to explore plausible large-scale motions without manually dragging parts of the model and losing track of what changed. Nonlinear normal modes offer a way to investigate those motions interactively and save conformations for further analysis.
SAMSON’s Normal Modes Advanced extension computes nonlinear normal modes using the NOLB algorithm. It is designed for biomolecular systems such as proteins, RNA, and DNA. In this workflow, the modes are a way to explore structural motion—not, by themselves, proof that a particular motion occurs biologically or that a pocket will bind a ligand.
Start with a structure and a focused question
Open a biomolecular structure in SAMSON; the tutorial uses the PDB entry 1VPK. Before calculating, decide whether to analyze the whole structure or a selected subset of residues. A focused selection can make sense when your question concerns a particular region, while a full-structure calculation lets you inspect broader movements.
Launch Normal Modes Advanced and choose the number of modes, the interaction cutoff distance, and the potential function. The interface currently provides the elastic network model potential. Once the calculation finishes, its results appear in the Output box.
Explore motion before choosing a conformation
Move a mode’s slider to display its motion on the structure. Each mode has a checkbox and a reset button. Check modes to combine them, then use play/pause to apply the selected motions. You can also adjust unchecked sliders while motion is playing; their changes are displayed in the trajectory too.
This makes it easier to compare candidate movements rather than treating the first visible opening as the answer. Try modes individually, then combine selected modes and inspect how the pocket and surrounding structure respond. The controls let you adjust the motion amplitude with a scaling factor, choose linear transformations (translations only) or nonlinear transformations (translations and rotations), and change motion speed. Harmonic motion can be enabled or disabled, and forward/backward step buttons help you inspect the trajectory one step at a time.
Real-time minimization can also be activated during motion, with one of three available minimization algorithms. Treat minimization as part of the exploration workflow: compare the resulting structures and decide which conformations are useful for your next analysis. The tutorial also shows how to reset individual sliders or all sliders, clear checked modes, and apply slider values to the structure with Update.
Define what “open” means for your pocket
When visual inspection is not enough, use the Structure Definition tab to define a target structure and find a combination of modes that reaches it. The definition can contain residues or atoms. This gives you a more specific objective than simply moving sliders and hoping to see an opening: identify the target arrangement you want to explore, then use the module to search for a mode combination that approaches it.
Keep the result in a form you can use
There are several ways to preserve an interesting result, and they serve different purposes. Save a conformation in the SAMSON document with the S shortcut if you want to restore that state quickly. If you need to superpose multiple structural states, create a SAMSON structural model instead; select the whole structure or the relevant part and use the Create button in the app. You can also export the current structure as a PDB file.
For a sequence of structures, open the Save Frames tab, set a saving interval, and store the frames as conformations or export them as PDB files. Alternatively, use Path to store the trajectory in a SAMSON trajectory node. Double-clicking a conformation or trajectory node displays it, and trajectory playback can be started or paused by double-clicking the trajectory node.
Before saving, check the calculation settings: the stored trajectory and conformations reflect the checked modes, their slider values, the scaling factor, the motion type, and the saving interval. Keeping these settings in mind makes it easier to reproduce the exploration and understand what a saved sequence represents.
For pocket-opening exploration, a practical sequence is: calculate modes, inspect individual motions, combine promising modes, define a target if you have one, and save the conformations or trajectory you want to analyze further. Continue with path generation, structural analysis, or simulation as appropriate—without treating an exploratory motion as a validated biological pathway.
See the original Normal Modes Advanced tutorial for the complete walkthrough and additional examples.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.