Not so long ago someone posted this link in this bord:
http://www.charite.de/bioinf/strap/
It convinced me.
Maybe that should also be included in the CCP4wiki a collection of what
program do I use when I want to make X Y or Z
Juergen
Ashley Buckle wrote:
I can recommend MUSTANG: http://p2
Hi Stephen,
please check the links in CCP4 wiki at
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Structure_based_sequence_alignment
best,
Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183
Fachbereich
I can recommend MUSTANG: http://p2p.cs.mu.oz.au/mustang/
Web server version is http://p2p.cs.mu.oz.au/mustang/php/
paper is here:
http://www.ncbi.nlm.nih.gov/pubmed/16736488?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
Ashley
On 05/03/2008, at 6:13 AM, Step
Dear all,
Thanks very much to everyone who replied. A tip-off from Petr Leiman
led me towards UCSF Chimera, which was able to generate a multiple
alignment file from my 4 superposed PDB files. Protocol for the
interested:
Open up Chimera and from the menu select "Tools" -> "Structure
Compariso
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
IL PROTECTED]
> Subject: Re: [ccp4bb] multiple sequence alignment from multiple pairwise
> structural alignments
> To: CCP4BB@JISCMAIL.AC.UK
>
> On Tuesday 04 March 2008 11:13, Stephen Graham wrote:
> > Hi all,
> >
> > I would like to generate a structure-base
On Tuesday 04 March 2008 11:13, 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
Hi Stephen,
Fun question! A quick google search with "structure based sequence
alignment" gave me this site which looks promising:
http://www.cgl.ucsf.edu/home/meng/grpmt/structalign-content.html
Let me know how it turns out!
Sophia
On Tue, Mar 4, 2008 at 11:13 AM, Stephen Graham <[EMAIL PROTEC
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
