Try ProSMART www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/prosmart/prosmart.html
etheses.whiterose.ac.uk/2120/ Conformation-independent comparison of protein structures Nicholls, Robert Adam (2011) Conformation-independent comparison of protein structures. PhD thesis, University of York. On Jul 13, 2012 11:37 AM, "Christian Roth" < christian.r...@bbz.uni-leipzig.de> wrote: > On Jul 13, 2012, at 4:00 PM, Christian Roth wrote: > > I want align a couple or protein structures by secondary structure > matching to > one target and want get a kind of aminoacid alignment file e.g. what > residue fit > the other, without adjustments due to sequence based alignments. > I tried Strap, but as far as I understood it, it takes also the sequence > into > account. I tried also Rapido, but this does only a pairwise comparison. > Superpose does align it nicely (ccp4 based or Coot based) but there seems > to > be no option to print the sequence alignment in a file and it is again > just a > pairwise comparison . > Is there an other program which does something similar? > > > If you use UCSF Chimera (www.cgl.ucsf.edu/chimera), you can use the > MatchMaker tool to superimpose the structures. MatchMaker allows you to > adjust the weight of sequence similarity vs. secondary structure matching, > so you can just make the sequence similarity 0% and the secondary structure > 100%. With the structures superimposed, you can use the Match->Align tool > to generate a sequence alignment based solely on the proximity of residues > to one another in space. Be warned that Match->Align will be very slow for > 10+ structures, but is fine for half a dozen or so. The generated > alignment will be displayed in a window that will have a "File" menu where > you can save the alignment to a variety of common formats. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >
