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?

  • 1
    $\begingroup$ I’m voting to close this question because it is not about a biological process or mechanism. $\endgroup$ – tyersome Mar 29 at 18:24


Start with a homologous protein. This protein can be thought of as two parts: (1) a backbone conformation and (2) a sequence of amino acids attached to the backbone. Threading occurs when you switch out the amino acids to those of your protein with unknown structure, but do not change the backbone conformation.

I believe the origin of the term is like beads on a string. The "string" does not change (the backbone geometry stays the same) but new "beads" (amino acids) are threaded onto certain positions.

The definition of superposition you found online is the correct definition for RosettaCM.

  • $\begingroup$ Welcome to Biology.SE! From How to Answer effectively in the help center, Answer well-asked questions. Not all questions can or should be answered here. This question is off-topic since it is not about a biological mechanism or process. Please consider deleting this answer and focusing on crafting well referenced answers to appropriate questions in the future since otherwise you are encouraging questions that are not suitable for this site. ——— Please take the tour and then consult the help center pages for additional advice on How to Answer effectively on this site. Thank you! $\endgroup$ – tyersome Mar 27 at 7:09

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