calculate RMSD

most of the program will superimpose the whole molecule.

some of them give me error message when align our proteins.
ex:Combinatorial Extension (CE) in strap

After all, according to this slides, I use Swiss-PdbViewer .

easy to use by hand, but I'm not sure how to make it calculate RMSD by program automatically.

1. download/load pdb file manually.
2. select residues on the right
3. fit/fit molecule (from selection)
done.

protein annotation tools (for machine learning purpose)

protein annotation tools (for machine learning purpose)
http://systers.molgen.mpg.de/cgi-bin/info.pl
http://pir.georgetown.edu/pirwww/search/batch.shtml
http://www.pir.uniprot.org/search/batch.shtml

already tried motif 1D to see if they have anything in common between proteins in fold#1,#2,#8, but there’s nothing in common.