RosettaCM

[Anonymous]

Hello, everyone!

I have a question about the RosettaCM Monte-Carlo sampling. I know, that it is not a problem with a program, so it is not for forum, but I hope for the best!

In the article it is written that “A Monte Carlo trajectory is carried out with two types of moves. (1) Substitution of the backbone torsion angles of a randomly selected Rosetta de novo fragment for the current torsion angles of these residues, and regeneration of coordinates according to the fold tree”. 

However, I from this article I couldn’t understand where the “current torsion angles” come from? Do they run molecular dynamics which create new conformation with new torsion angles? 

Thank you in advance,

Dmitrii.

[Anonymous]

It’s Monte Carlo, so it performs many, many cycles of moves as it goes.

For all cycles but the first, “current torsion angles” means whatever torsions angles were the result of the previous Monte Carlo cycle.

For the first cycle – torsions come from the templates.  This is comparative modeling, not de novo – so there is a template for most residues, and the rest are filled in somehow (probably via loop modeling). 

[Anonymous]

It’s Monte Carlo, so it performs many, many cycles of moves as it goes.

For all cycles but the first, “current torsion angles” means whatever torsions angles were the result of the previous Monte Carlo cycle.

For the first cycle – torsions come from the templates.  This is comparative modeling, not de novo – so there is a template for most residues, and the rest are filled in somehow (probably via loop modeling). 

[Anonymous]

It’s Monte Carlo, so it performs many, many cycles of moves as it goes.

For all cycles but the first, “current torsion angles” means whatever torsions angles were the result of the previous Monte Carlo cycle.

For the first cycle – torsions come from the templates.  This is comparative modeling, not de novo – so there is a template for most residues, and the rest are filled in somehow (probably via loop modeling). 

[Anonymous]

If I understood you right, during the modeling the whole protein changes guided by the physically-realistic energy function and template-derived constraints, and in the end of each “change” the random replacement of torsion angles happens. Is it right?

[Anonymous]

If I understood you right, during the modeling the whole protein changes guided by the physically-realistic energy function and template-derived constraints, and in the end of each “change” the random replacement of torsion angles happens. Is it right?

[Anonymous]

If I understood you right, during the modeling the whole protein changes guided by the physically-realistic energy function and template-derived constraints, and in the end of each “change” the random replacement of torsion angles happens. Is it right?

[Anonymous]

The random Monte Carlo cycle changes ARE the backbone torsion angles changing.  (The sidechain torsions change too, but those are less significant).  What else would be changing if not the torsions of the backbone?

[Anonymous]

The random Monte Carlo cycle changes ARE the backbone torsion angles changing.  (The sidechain torsions change too, but those are less significant).  What else would be changing if not the torsions of the backbone?

[Anonymous]

The random Monte Carlo cycle changes ARE the backbone torsion angles changing.  (The sidechain torsions change too, but those are less significant).  What else would be changing if not the torsions of the backbone?

[Author]

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