Binding Probe Puzzles
|Opened on:||Saturday, April 7, 2012 - 06:10|
|Last modified:||Monday, April 9, 2012 - 18:46|
I'm enjoying these little design puzzles. I think 3 residues is a good size for the binding probe. Would it be possible to leave the protein backbone frozen, but to unfreeze the sidechains near the binding site? it's annoying to be just out of range of some great big flimsy lysine.
The small ligand wiggles slowly....I've literally watched it go up by 0.001 point per second for 90 minutes. Looks like jumping in with a local wiggle speeds that up though, but I'll have to modify scripts to do a local wiggle instead of a global wiggle. I miss the wiggle slider (sounds of teeth gnashing as people read this).
Anybody else have any comments?