protein structure alignment in 3D - (Nov/21/2008 )
Hello,
I am looking for an alternative program to Secondary-structure matching (SSM) (
http://www.ccp4.ac.uk/ccp4bin/viewcvs/ccp4/lib/ssm/ ) to computes protein structure alignment in three dimensions.
It would be great if the alternative program is implement in C or Java.
Best regards,
DALI - MSD
SAP
SAP
Do you know where can I find the code of DALI, MSD and SAP?
This may come across as being a tad harsh but, did you look for yourself?
I googled protein structure alignment and found this http://en.wikipedia.org/wiki/Protein_structural_alignment as the first hit.
I then read that article and found links to several alignment methods.
A good resource that is harder* to find is the EBI resources page - this has tools for all sorts of things.
*Actually it isn't hard at all 
I wouldn't suggest digging into the SAPP source unless you are a proficient c coder or it has been significantly rewritten.
Also look at this:
http://peds.oxfordjournals.org/cgi/content/full/13/11/745
There is a somewhat old paper that covers several tools including those cited in the wikipedia link above - you really should find the paper.