I'm a beginner in structural biology.
I had a question while reading a paper on RosettaCM.
What does RosettaCM's superposition and thread mean?
I googled it.
As a result, the following results were obtained.
The term structural superposition refers to rotations and translations performed on one molecular structure to make it match another structure or structures. Inherent in the definition of structural superposition is an assumed measure of structural similarity. The optimal superposition is the one in which this similarity measure is maximized. Alternatively, one can define superposition in terms of a difference measure, such as root-mean square deviation ( RMSD ). In this case, the optimal superpositon is one in which the RMSD is minimized. The program ASH uses the former approach with similarity defined by the NER score.
Also, implied in any superpositon is an alignment, or mapping, between points in one structure (usually atoms) and those in another. Sometimes alignment and superpositon are used interchangeably.
Is this correct?
I also think of threads as part of a protein segment, is this correct?
In other words, in Rosetta CM's 1-step Global Superpotion, after aligning, the templates are stochastically determined, and the unselected templates are superposed so that RSMD is smallest.
Furthermore, the superposed template is a thread.
Is the above correct?