Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?

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CCP4bb <-- 2007 <-- December 2007 <-- 05 December 2007

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Subject: Re: How to make a structure-based multiple sequence alignment on DALI server?
From: Klaus Futterer k {- dot -} futterer {- at -} BHAM {- dot -} AC {- dot -} UK
Date: 2007-12-05

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Subject: Unidentified ligand (electron density) found at active site
From: Ronaldo Alves Pinto Nagem nagem {- at -} ICB {- dot -} UFMG {- dot -} BR
Date: 2007-12-05

Subject: Re: How to make a structure-based multiple sequence alignment on DALI server?
From: Brenda Patterson ucbccka {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2007-12-05

POSA at the Godzik lab does exactly what you are after, flexibly!

http://fatcat.burnham.org/POSA/

>> Hi all=A3=AC
>>
>> I want to produce structure-based multiple sequence alignment of my =20=
>
>> protein with five of its homologs on DALI server. However, when I =20
>> tried the "Database Search Form", only one homolog was picked up =20
>> from PDB. If I align my protein with each homolog by the "DaliLite =20
>> Pairwise comparison", how can I combine them together?
>>
>> Thanks in advance.
>>
>>
>> Best regards,
>> =09
>> Sincerely,
>>
>> Dalei Wu
>> Drug Discovery and Design Center
>> Shanghai Institute of Materia Medica
>> Shanghai Institutes for Biological Sciences
>> Chinese Academy of Sciences
>> 555 Zu Chongzhi Road, Shanghai, 201203, China
>> david.dlwu@gmail.com
>> 2007-12-05
>

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CCP4bb <-- 2007 <-- December 2007 <-- 05 December 2007

Next message:
Subject: Unidentified ligand (electron density) found at active site
From: Ronaldo Alves Pinto Nagem nagem {- at -} ICB {- dot -} UFMG {- dot -} BR
Date: 2007-12-05