Re: [ccp4bb] protein sequence database with conservation score annotation

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

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Subject: protein sequence database with conservation score annotation
From: å•†å…ƒ shangyuan5000 {- at -} GMAIL {- dot -} COM
Date: 2012-08-22

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From: Arnaud Goepfert arnaud {- dot -} goepfert {- at -} UNIBAS {- dot -} CH
Date: 2012-08-22

Subject: Re: protein sequence database with conservation score annotation
From: Robbie Joosten robbie_joosten {- at -} HOTMAIL {- dot -} COM
Date: 2012-08-22

Dear Yuan Shang,

HSSP provides multiple sequence alignments with conservation scores per
position. It is originally PDB derived in the sense that a multiple sequence
alignment already exists for each PDB entry. You can also make HSSP entries
from sequence alone, but you should contact the HSSP maintainers because I$B!G(B
m not sure this service is public yet. You can also cheat a bit and just get
the HSSP for the closest homologue in the PDB.

HTH,

Robbie Joosten

Netherlands Cancer Institute

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ??
Sent: Wednesday, August 22, 2012 06:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] protein sequence database with conservation score
annotation

Hi,everyone,

Does anyone here could recommend such a database for me? I've searched
the web and only find tools like 'consurf'. Databases like 'consurf' are
important for the analysis of the current known structures. However, for the
original discoveries of new domains, sequence databases with such
conservation score annotation could be as important as the secondary
structure prediction.

Although the 'conservation score' maynot be as accurate as that from the
'consurf database' which is based on the 3-D alignment. The information of
such database could be much more helpful, especially for some new proteins,
or proteins regions without any structure available.

Best regards,

Yuan SHANG

HKUST

CCP4bb navigation

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

Previous message:
Subject: protein sequence database with conservation score annotation
From: å•†å…ƒ shangyuan5000 {- at -} GMAIL {- dot -} COM
Date: 2012-08-22

Next message:
Subject: Re: Purify non-stable protein
From: Arnaud Goepfert arnaud {- dot -} goepfert {- at -} UNIBAS {- dot -} CH
Date: 2012-08-22