On Mon, March 5, 2007 2:16 pm, Nat Echols wrote: > I had a debate with a coworker about using MR in desperation and I'm > curious what the most extreme case is where a very different model was > used to solve a structure. This could be highest RMSD, lowest % identity, > or most incomplete model. I'm also curious whether homology modelling has > ever been useful for this. (I'm pretty sure I've come across papers > discussing this last concept.) > > thanks, > Nat >
I'm not sure what "in desperation" means. You're trying to solve a structure, so all options are open, right? They don't have to be elegant, it just has to work. :) I know of a few cases where roughly 15% of a structure was used as a search model to solve a structure. Recently I used about 30% of the structure to get the initial model with MR, and then bootstrap along to find the remainder. Similarly, you can get away with 25-30% sequence homology (so long as there is high structural homology) with MR. It's relatively easy to find a helix-turn-helix motif by MR than, say, an extended beta-sheet expanse, because the beta-sheet can substantially bend and twist, whereas the helices are fairly rigid. Bernie Santarsiero
