You might want to have a look at consurf, which maps conservation from an alignment onto a structure. http://consurf.tau.ac.il/ On 23/06/2011, at 6:42 PM, Simon Kolstoe 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
