About: Ideal Loops   Sponge Permalink

An Entity of Type : owl:Thing, within Data Space : 134.155.108.49:8890 associated with source dataset(s)

One of the goals of Foldit is to design new proteins that fold up spontaneously the way natural proteins do. To date, efforts to design self-folding proteins in Foldit have not been successful. Foldit researchers have identified "ideal loops" as one way to make player-designed proteins more likely to behave like natural proteins. "Loops" are of course sections of a protein that lack a specific secondary structure. Often, relatively short sections of loop connect sections which have a secondary structure of sheet or helix. (In other cases, a long, meandering loop may connect sheets and helixes.)

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  • Ideal Loops
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  • One of the goals of Foldit is to design new proteins that fold up spontaneously the way natural proteins do. To date, efforts to design self-folding proteins in Foldit have not been successful. Foldit researchers have identified "ideal loops" as one way to make player-designed proteins more likely to behave like natural proteins. "Loops" are of course sections of a protein that lack a specific secondary structure. Often, relatively short sections of loop connect sections which have a secondary structure of sheet or helix. (In other cases, a long, meandering loop may connect sheets and helixes.)
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abstract
  • One of the goals of Foldit is to design new proteins that fold up spontaneously the way natural proteins do. To date, efforts to design self-folding proteins in Foldit have not been successful. Foldit researchers have identified "ideal loops" as one way to make player-designed proteins more likely to behave like natural proteins. "Loops" are of course sections of a protein that lack a specific secondary structure. Often, relatively short sections of loop connect sections which have a secondary structure of sheet or helix. (In other cases, a long, meandering loop may connect sheets and helixes.) Short sections of loop often involve a sharp turn. For example, a loop containing only two segments may connect two sheets in an "antiparallel" arrangement. Analysis of natural proteins has revealed common patterns in these short sections of loop, which has lead to the concept of "ideal loops". Two scientific papers, Principles for designing ideal protein structures (published in Nature in 2012), and Control over overall shape and size in de novo designed proteins (published PNAS in 2015), are the basis of the ideal loops concept in Foldit. In particular, Foldit black-belt player Susume recommends Figure 1 and Figure 2 of the 2012 Nature paper. For the 2015 PNAS paper, Susume cites Figure 4 as a good starting point. Several recent changes in Foldit are intended to promote the use of ideal loops in Foldit design.
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