I ended up using multiprot and staccato recently
http://bioinfo3d.cs.tau.ac.il/MultiProt/
There is a server for multiprot, but I downloaded the applications. I
still ended up doing quite a bit manual editing in filling the gaps in
the structures etc.
I stumbled also over a link about the matter comparing different
programs (by Dr Elaine Meng):
http://www.cgl.ucsf.edu/home/meng/grpmt/structalign-content.html
~L~
______________________________________________________
Lari Lehtiö
Pharmacy, Department of Biochemistry and Pharmacy
Åbo Akademi University,
BioCity, FIN-20520 Turku
Finland
+358 2 215 4270
http://www.users.abo.fi/llehtio/
______________________________________________________
Quoting Ronnie Berntsson <r.bernts...@rug.nl>:
Dear all,
A bit off the topic question perhaps.
I am trying to find a program which can do multiple structural
sequence alignments. What I would like is a program which can take
as input PDB codes (or files), and which will output a multiple
sequence alignment in FASTA format with the full sequences of the
supplied proteins intact. Preferably said server/program should be
able to handle at least 20 input pdbs at once.
I've been looking around, but have so far failed to find a program
which does this. If anyone knows of a program or server which could
handle this, I would be very grateful.
Cheers,
Ronnie Berntsson
