Fold It! Rebuild tool

Sunday, May 23, 2010

Fold It! Rebuild tool

Brief video to show how the rebuild tool in Fold It! works. fold.it Here's a narrative to help those non-native English speakers that will find it easier to translate. "Hey it's Feet1st here. I thought I'd make a little video to show you how to use the new "rebuild" tool. I'm working on the third CASP8 target, a very complex protein with a lot "going on". I want to rebuild this area here, this connector tube. What I'm going to do is lock out, by middle clicking (or you can hold the shift key and left click), a small portion of the backbone here. Then right click on it, and "rebuild". ...we have our wonderful music, and you sit back and relax... 27593 is the score I had when I stared the rebuild. It's going to go through different combinations of this sequence of amino acids, and orientations they might typically take in a native protein. When it finds a combination that matches the beginning and end position, it will transition to that, and show you that shape. ...So, you've seen it shift a couple of times now. Those are combinations that fit this puzzle. And the score will go up or down, either way, depending on the goodness of that fit, and the resulting scores of the side chains, and the conflicts that might resolve, or might be introduced by the new shape. ...so typically what you are doing is you are going to rebuild, ...oh I love the "rank down"... and just play back to your best score. That will be the configuration that probably resolved a conflict or worked best ...