You might find the PHYRE server useful. It can also deal with gaps and loops. Can be useful for prepping MR models, too.
Roger Rowlett On Jun 23, 2011 4:42 AM, "Simon Kolstoe" <[email protected]> wrote: > Dear ccp4bb, > > One of my colleagues is interested in how a certain protein differs between species. He's done a blast search, collected all the aligned sequences, and "emailed them to the crystallographer to tell him the implications of the sequence changes". > > Although I am not at all confident that I can predict any implications based upon sequence differences, I thought I could at least have a try by mapping the different species sequences onto the existing structure and then regularising it just to see what happens (and then perhaps looking at buried surface area, electrostatics, subunit interfaces etc.). > > I know the program chainsaw can mutate the sequence based on an alignment, however I can't stop it pruning non-conserved residues. Does anyone know of another program that I could use to do this step? > > Similarly if anyone knows other software tools/methods I could use to try and work out the implications of sequence changes I would be grateful for advice. > > Thanks, > > Simon
