Hi,
Is there a program out there where I can feed a protein backbone, or any kind of linear chain and will tell me whether it has formed a knot?
Whats even better, is a program that can read two protein backbones, and can tell me if the two proteins have the same topology(i.e. can wiggle around to match each other without unfolding and refolding).
Thanks, Morakano Taka
You might be better off in a biologically oriented newsgroup than here, but since you asked:
Protein folding is still a largely unsolved problem both from a kinetic and thermodynamic viewpoint. Knots are even nastier to hypothesize about - keep in mind that the knots you speak of are different than the knots that mathematicians speak of (the latter use closed loops).
While there might be a case or two that have been solved for the questions you asked (most likely with small proteins), a univsersal solution does not exist at this time.
John Aspen Research, -
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