Hand folding de novo

marie_s strategyEdit

De novo without structure

Foldit 1374440930

finding the loops

Define what are the loops : by finding proline, glycine, arginine, a group of 2 lysines and the 3 to 5 segments around them.

First, fold your protein so you can view it. One way is to join each methionine or phenylalanine with a band with the next methionine or phenylalanine. Then use the wiggle function. Finally, rebuild each structure to decide if it its an a-helix or a b-sheet.

After that, move and rebuild the structure to find a shape that look good. Keep the protein large to rebuild and move the part. As the protein is large, sheets and helices can be tweaked and rebuild without problems. Let the protein explode a little, it shows you what it is stable and not stable and the protein can find a better shape by itself. All the folding is done with CI=1, bands at the length by default, no more than 6 bands at the same time. Until the score is > 10 200 the improvements need large rebuilds, so shift sheets that could not have been done by a script.

When the score is > 10,200, try to shake at low CI to sort the side chains a little.

In fact, after this work , fusing give few points.

Some improvements put the protein to a good score (rank 12, one day before the end), the structure is not the same at the initial one for this puzzle.

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