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How to start folding a DeNovo (freestyle) puzzle?

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[Adapted from discussion on #global with itskimo and others]

Start by shaking wiggling side chainsEdit

but do not move the backbone just yet. First define the secondary structures.
These are the Sheets, Helices, Loops. Then freeze the Sheets and Helices.

Denovo 1





Next by wiggling the backbone the protein well start to bend.
Start the ci= low and then slide up higher as it starts to fold together.
So help it to fold at the bends by banding between the frozen sheets.

Capture 2






Fold it up.

Capture3








Add more bands between the frozen sheets and also going out to the sides.

Capture4










These extra bands well help to anchor the protein and keep it flat.

Capture26


Capture25































As the protein starts to fold up help it along.Edit

Try to keep it flat and from making a huge knot. Keep the sheets frozen and band between them.

Capture5











Now the protein starts to come together, wiggle for a while at ci= 0.05 rising the value slowly.

Capture6


http://fold.it/portal/files/chatimg/irc_192195_1299872358.png
Usually the protein gets stuck at this point but, remember orange in blue out.
Then try wiggling and getting the sheets better aligned and then Tlaloc hydro or
repeat settle and others to keep things together seems to work well.

Now for a helixEdit

First freeze the whole protein and then unfreeze the parts we well be working on.
Also unfreeze the end loops to give the helix room to form and move.

Capture7


http://fold.it/portal/files/chatimg/irc_192195_1299872637.png
Next build the helix by defining the secondary structure as a helix and rebuilding.

Capture8



http://fold.it/portal/files/chatimg/irc_192195_1299872721.png
After a nice helix forms stop it.

Capture9
















http://fold.it/portal/files/chatimg/irc_192195_1299872777.png
There are lots of conflicts so do wiggles first.
By using a low ci= at first and then raising the ci= value the conflicts become less.
Now freeze the entire protien and unfreeze the other side for the next helix.

Capture10

http://fold.it/portal/files/chatimg/irc_192195_1299872948.png
On this side we well have to define the structure as a heliix first.

Capture11

http://fold.it/portal/files/chatimg/irc_192195_1299873034.png
And then rebuild to make the helix form.

Capture12
http://fold.it/portal/files/chatimg/irc_192195_1299873062.png

After rebuilding for a while we get a good helix. This helix can be frozen to help hold its shape.

Capture13

http://fold.it/portal/files/chatimg/irc_192195_1299873235.png

Now we try to put it all togetherEdit

By unfreezing most of the protien but leaving the sheets frozen to keep them flat. The helix can be frozen also to keep them streight. The loops should be unfrozen so they can flex and twist as the protein starts to settle.
In the middle of te protein you can see a helix that wants to be a sheet so we well redefine it and make it so.

Capture14


http://fold.it/portal/files/chatimg/irc_192195_1299873372.png
After you get the sheet streight freeze the new sheet and wiggle some more.

Capture15


http://fold.it/portal/files/chatimg/irc_192195_1299873499.png
Hopefully the helix well settle into a good position. And you are on your way.

Capture16


http://fold.it/portal/files/chatimg/irc_192195_1299873544.png
Some of the sheets are comming together better forming bonds.

Capture17


http://fold.it/portal/files/chatimg/irc_192195_1299873605.png

Remove some bands and hope it stays together.Edit

Capture24




http://fold.it/portal/files/chatimg/irc_192195_1299873778.png
Wiggle shake sidechains and run something like a walker or bander script
like tlaloc repeat seatle or tlaloc hydro or contract
So here it is not great but it was fast.
Now we need to take more time lineing up the sheets better.

Capture19

http://fold.it/portal/files/chatimg/irc_192195_1299874055.png

Capture20

http://fold.it/portal/files/chatimg/irc_192195_1299874341.png
By running scripts the protein is able to compact a bit more but there are still some annoying voids.

Capture21


http://fold.it/portal/files/chatimg/irc_192195_1299874610.png
Another with mostly sheets
http://fold.it/portal/files/chatimg/irc_192195_1299874714.png

Capture22


http://fold.it/portal/files/chatimg/irc_192195_1299875435.png
Could use some more sheet work. Once the bonds are well formed it should stabilize.
Then a quick rebuild of the helices to coil them up a bit better.

Capture23


http://fold.it/portal/files/chatimg/irc_192195_1299875819.png

Here is a way to move a helix through a frozen protienEdit

Fist freeze protien and unfrees the helix and loop that you want to move to the
other side. Then band to where you want the helix to be and rebulid
http://fold.it/portal/files/chatimg/irc_192195_1299879263.png http://fold.it/portal/files/chatimg/irc_192195_1299879296.png


See a video by Phallicies with cut points

http://www.youtube.com/watch?v=5750OScmWpE

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