Re: [ccp4bb] multiple sequence alignment from multiple pairwise structural alignments

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Removal of glycosylation sites in Picha expression construct
From: artem {- at -} XTALS {- dot -} ORG artem {- at -} XTALS {- dot -} ORG
Date: 2008-03-04

Next message:
Subject: Re: multiple sequence alignment from multiple pairwise structural alignments
From: Stephen Graham stepheng {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-03-04

Subject: Re: multiple sequence alignment from multiple pairwise structural alignments
From: Joao Dias jmdias {- at -} SCRIPPS {- dot -} EDU
Date: 2008-03-04

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
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Removal of glycosylation sites in Picha expression construct
From: artem {- at -} XTALS {- dot -} ORG artem {- at -} XTALS {- dot -} ORG
Date: 2008-03-04