How about this server
http://iris.physics.iisc.ernet.in/psap/
> On 10/29/2013 03:23 AM, Katherine Sippel wrote:
>> Hi all,
>>
>> I was wondering if anyone knew of a software or server to mine the PDB
>> for a specific class of interactions? I've tried PDBeMotif without much
>> luck and I though
Yes, this is a result of some imperfectness in shared build (6.3.0 was static).
The bug should have been fixed in updated release bundles, and also in the
recent update.
Eugene
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Dmitry Rodionov
On 10/29/2013 03:23 AM, Katherine Sippel wrote:
Hi all,
I was wondering if anyone knew of a software or server to mine the PDB
for a specific class of interactions? I've tried PDBeMotif without much
luck and I thought I'd check to see if there was an alternative before I
go re-inventing the whee
Katherine
I am not exactly sure what sort of tool you would like to use, but there are
a couple of options found here...
http://www.ebi.ac.uk/pdbe-as/pdbetemplate/
The last option DB search
http://www.ebi.ac.uk/pdbe-as/pdbesearch/
allows you upload a fragment of structure - a small number of r
As Juergen has mentioned, both the T200 and the BioRad ProteOn (XPR36) are good
options (we have both).
The XPR36 is a higher throughput machine and can also be used for small
molecule work (not quite as sensitive as the T200, but more sensitive than we
had anticipated and certainly higher throu
I don't know whether your question is specifically for protein-ligand
interactions, protein-protein interactions, internal protein interactions,
etc., but one place to start is to look at some of the database tools already
available on-line, including, for example, CREDO from Tom Blundell's grou
Another option is BLItz which is cheaper and uses interferometry.
Dee
Date: Mon, 28 Oct 2013 11:05:33 -0400
From: jubo...@jhsph.edu
Subject: Re: [ccp4bb] Biacore/SPR
To: CCP4BB@JISCMAIL.AC.UK
BiaCore 3000 or if you can afford the T200.Proteon XPR36 would be a cheaper
Option and should work as w
Hi all,
I was wondering if anyone knew of a software or server to mine the PDB for
a specific class of interactions? I've tried PDBeMotif without much luck
and I thought I'd check to see if there was an alternative before I go
re-inventing the wheel.
Cheers,
Katherine
--
"Nil illegitimo carboru
Thanks for the suggestions!
I just opened a new terminal window, and it appears that problem had
disappeared (by itself?).
Sorry for the false alarm- I'll go see a mental health professional.
Best regards,
Dmitry
On 2013-10-28, at 12:49 PM, William Scott wrote:
> It looks like it should
I had this problem last week but it seems to have been solved by reinstalling
the ccp4 6.4.0 package today, slightly updated I believe
There was message from Eugene Krissinel which may be relevant to this
Phil
On 28 Oct 2013, at 16:00, Dmitry Rodionov wrote:
> Good day!
>
> I'm having proble
It looks like it should be doing the right thing, i.e.,
zsh-% otool -L qtrview
qtrview:
@executable_path/../Frameworks/QtWebKit.framework/Versions/4/QtWebKit
(compatibility version 4.9.0, current version 4.9.3)
@executable_path/../Frameworks/QtXmlPatterns.framework/Versions/4/Q
The Eighth International Workshop on X-ray Radiation Damage to Biological
Crystalline Samples will be held at the EMBL and DESY, Hamburg, Germany from
April 10th (13:00) to April 12th (13:00) 2014.
This series of workshops was originally concerned with the effects of radiation
damage during i
Good day!
I'm having problems with qtrview (on OS X 10.6): it crashes or hangs after
spitting out a screenful of messages like
objc[2975]: Class QCocoaMenu is implemented in both
/Applications/ccp4-6.4.0/bin/../Frameworks/QtGui.framework/Versions/4/QtGui and
/Library/Frameworks/QtGui.framework
Dear Dong,
Biacore T200 is the best choice for protein/small molecule interaction
analysis.
the Biacore 3000 works perfectly for protein-protein interactions.
hope that help you.
Badr
--
Dr Douzi Badreddine
Architecture and Function of Biological Macromolecules (AFMB), CNRS UMR7257
163 Avenue d
BiaCore 3000 or if you can afford the T200.
Proteon XPR36 would be a cheaper Option and should work as well.
Jürgen
On Oct 28, 2013, at 10:54 AM, Gang Dong wrote:
We mainly measure protein-protein interactions (sometimes protein-small
molecules). Thanks! _Gang
From: Bosch, Juergen [mailto:jubo.
We mainly measure protein-protein interactions (sometimes protein-small
molecules). Thanks! _Gang
From: Bosch, Juergen [mailto:jubo...@jhsph.edu]
Sent: Monday, October 28, 2013 3:17 PM
To: Gang Dong
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Biacore/SPR
Protein-protein interaction?
p
Protein-protein interaction?
protein-small molecule interactions ?
Epitope mapping of mABs ?
Could you specify what you would like to do, as different models are good for
different things.
Jürgen
On Oct 28, 2013, at 10:08 AM, Gang Dong wrote:
Dear all,
Could anyone tell me your experience with
Dear all,
Could anyone tell me your experience with Biacore (any models) or a similar
SPR-based technology for measuring interaction kinetics? I also want to know
the price ranges to discuss with our department/facility managers.
Thanks,
Gang
Just a quick off-topic question which people here may have experience in:
We have a protein which expresses with a GST tag. It has much poorer expression
without. When the tag is cleaved, the protein does not crash out but we are
having difficulty separating it as the proteins seem to stick toge
Well I would start by flipping the carbonyl oxygen then see if the
side chain can use the density - what are the B values for the
neighbouring stuff?
Eleanor
On 25 October 2013 19:00, Patel, Joe wrote:
> Is that a glycine in the sequence next to the Glu/Gln? Have you tried
> building a 50% occ
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