When modeling protein conformational transitions, a common source of frustration is making sure the start and goal conformations are properly set up in the simulation environment. If these aren’t prepared correctly, everything from calculations to visualization can fail or produce confusing results. In this post, you’ll learn a simple but essential step to correctly define and select these conformations using the Protein Path Finder app in SAMSON.
The Protein Path Finder assists researchers in discovering potential transition pathways between two protein conformations. This can be useful, for example, when investigating ligand-induced conformational changes or domain motions. However, a successful pathway search begins with proper definition of what ‘start’ and ‘goal’ mean in your data.
Step 1: Loading a Prepared Model
If you’re following the tutorial example, start by loading the predefined model from SAMSON Connect:
https://www.samson-connect.net/documents/5eb7990e-fa44-4595-ab2c-99b6c68eada9
You can paste this directly into Home > Download in SAMSON to load Adenylate Kinase with two conformations labeled as start and goal.
Step 2: Open the Protein Path Finder App
Go to Home > Apps > Biology and open Protein Path Finder. In its interface, find the Set up the system section and expand it.
Step 3: Get the Conformations
Click the button labeled Get conformations from the active document. SAMSON will retrieve all models (conformations) present in the loaded structure. These models are often represented using the MODEL and ENDMDL keywords in PDB files.
Once they appear in the lists below, select your start and goal conformations accordingly. These will serve as references for the motion planning algorithm.
Why This Matters
Correctly defining start and goal conformations ensures meaningful energy calculations and more interpretable transition pathways. It might seem like a minor step, but skipping or misconfiguring it can skew downstream analysis or increase the risk of the search algorithm failing to converge.
Although this might sound like a small part of the workflow, it’s one of those critical junctures where mistakes propagate quickly. Taking a few seconds to properly load and confirm the conformations can save hours of debugging later.
Tips for Custom Models
Working with your own protein model? Be sure both conformations are loaded into a single document as distinct models. You can merge them manually in a text editor if needed using the following format:
|
1 2 3 4 5 6 7 |
MODEL 1 ... ENDMDL MODEL 2 ... ENDMDL END |
This enables the app to correctly interpret start and goal conformations.
Ready to try it yourself? You can explore the full tutorial and more tools in the documentation center.
Access full documentation here
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.