Hi Stephen, I will add to the previously mentioned ones the MSD ssm server at EBI? http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver
You also have the Godzik tools if your proteins have flexible regions. FATCAT http://fatcat.burnham.org/ and POSA http://fatcat.burnham.org/POSA/ Good luck, Joao João M. Dias Ollmann Saphire Lab The Scripps Research Institute 10550 North Torrey Pines Rd. IMM-2 La Jolla, CA 92037 USA On Mar 4, 2008, at 11:13 AM, Stephen Graham wrote:
Hi all, I would like to generate a structure-based multiple sequence alignment using 4 structures. I have already generated pairwise alignments for each 'pair' of structures (6 alignments in all). Is there a program out there that can take a number of aligned structures (or even just a number of pairwise sequence alignments) and calculate the 'best' multiple sequence alignment? Please note that there is absolutely no sequence conservation between these structures, making standard sequence-based alignment tools pretty useless. Thanks, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
