Secondary Structure¶
Purpose¶
Secondary structure elements, such as alpha-helices and beta-sheets, are fundamental to a protein’s local conformation and overall fold. By tracking the formation, stability, and transitions of these secondary structures over time, this benchmark determines if the MLIP accurately maintains the protein’s native secondary structure or captures realistic conformational changes. Significant deviations in secondary structure match relative to the native structure provides a quantitative measure of its reliability for simulating protein systems.
The results are presented as the average values over the trajectory. Evolution of the metrics over time is additionally plotted.
Description¶
The secondary structure of proteins is determined using the DSSP (Define Secondary Structure of Proteins) algorithm [1], as implemented in the mdtraj Python package. For each frame of the molecular dynamics trajectory, the atomic coordinates are analyzed to assign secondary structure elements—such as alpha helices, beta strands, and coils—to each residue.
The implementation is as follows:
The trajectory is loaded as an mdtraj.Trajectory object.
The function
mdtraj.compute_dssp(traj, simplified=False)computes the secondary structure assignment for each residue and each frame.The same analysis is run for the reference structure
For each frame, the DSSP assignment is compared to the reference. A match is counted when both have the same DSSP code.
Interpretation¶
The secondary structure content should be as close to the reference as possible. The matching DSSP should be as close to 1 as possible.