A pair of protein structures gives you two snapshots, but not the motion that connects them. That gap matters when you want to explore a conformational transition: the endpoint structures alone do not show which route the protein might take between them. Protein Path Finder in SAMSON helps address this problem by searching for candidate transition paths between two conformations of the same protein.
The result is best treated as a useful path to inspect—not as proof that the protein follows that exact route in nature. The search uses ART-RRT, combining T-RRT for pathway search with ARAP for motion generation. Constrained minimization is applied as new states are generated to help keep motions physically reasonable within the chosen model and settings.
Start with compatible structures
A practical first step is to make sure the two conformations describe the same system. For this workflow, the structures need matching chains, residues, and atoms. If your conformations are in separate files, prepare them individually and combine them as separate models in one PDB file. For your own system, preparation may include removing alternate locations, ligands, solvent, and ions, and adding hydrogens. If residues or heavy atoms are missing, the PDBFixer extension can help fix the protein.
Once the structures are available in SAMSON, select them as the start and goal conformations. The tutorial’s sample document uses two conformations of adenylate kinase, from the 4AKE and 1AKE structures. Starting with the sample is a straightforward way to learn the workflow before adapting it to another protein.
Choose what controls the motion
One important modeling choice is which atoms are active in the ARAP method. Active atoms control the protein motion; the remaining atoms are passive and follow them according to the ARAP method. In the sample, two backbone alpha-carbon atoms are selected: the CA atoms in GLY 12 and ARG 123. This gives the search selected points to work with rather than treating every atom as an independent motion control.
The appropriate active atoms depend on the transition you are investigating. Think about which regions or points should guide the motion, and inspect the selection in the document before running the planner. In SAMSON, you can select atoms in the document and add them as active atoms in the app. The app also lets you review or reset that assignment.
Set up energy evaluation before searching
The tutorial uses the Universal Force Field (UFF) as the interaction model and FIRE as the state updater. The system should already be minimized; SAMSON’s Edit > Minimize command uses UFF for minimization. When setting up UFF, the tutorial chooses to use existing bonds. It also sets the FIRE step size to 1 fs and the number of steps to 1. These are workflow settings from the tutorial, not a universal recipe for every protein or modeling goal.
Understand the search controls
The sampling box defines the region in which the active atoms are sampled. Its position and size influence their motion and therefore the paths found. The tutorial uses a 200-angstrom cube. A box that is too restrictive may constrain the search; a larger box gives more room to explore, but the appropriate dimensions depend on the system and the transition you want to investigate.
Search parameters also affect the results. The tutorial runs the planner twice to seek up to two paths, with 20 ARAP-modeling iterations and 20 constrained minimization iterations for each newly generated state. The T-RRT settings include an initial temperature, a temperature factor, and a failure count before increasing the temperature; the RRT extension step size controls how far the search extends. A fixed seed makes a run reproducible for the same seed, while an unchecked seed option uses a random seed. If alignment to the start conformation is enabled, it can make the search faster, although the documentation notes that artifacts can occur in rare cases.
During a run, the Advanced information panel reports items such as elapsed time, the number of tree nodes, the current run, and paths found. These are useful for monitoring progress, but they do not by themselves tell you whether a path is suitable for your scientific question.
Inspect and carry forward the paths
Found paths appear in the Results tab. Select a path to inspect its energy curve and move through its conformations with the slider. The selected conformation appears in the viewport, and its energy is shown in the UFF window. When comparing candidates, the table includes the number of states, minimum and maximum energies, a saddle value (maximum minus minimum), and a barrier value (maximum minus the first energy), along with timing and other details. These are model-dependent quantities and should be interpreted in the context of the selected interaction model.
You can copy table data or path energy values, export paths into the document as trajectories, or export selected conformations at an interval you choose. For further refinement, the documentation points to P-NEB as a way to improve paths, and to the Export Along Paths app for exporting trajectories of selected atoms.
For the complete workflow and its settings, see the Protein Path Finder tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.