I would recommend Modeller
http://www.salilab.org/modeller/
Wai
Suppose I have two proteins A and B, they are structurally homologous,
however the sequence identity is only about 20%. A has crystal
structure available, so if I want to model protein B, what's the best
way to do it? I don't
Hi Rui
Very easy to use is EsyPred3D :
http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/
Also good performance server is 3d-JIGSAW :
http://bmm.cancerresearchuk.org/~3djigsaw/
Hope it helps
Cheers
Francisco
Hi, All
Suppose I have two proteins A and B, they are structurally
Modeller is indeed an excellent program (so are some others) but,
without being an expert, I was told some time ago and I am still under
the impression, that homology modeling with 20% identity (and many
insertions and deletions as you point out) is a dark art. Being able
to suggest the
Try Phyre (http://www.sbg.bio.ic.ac.uk/phyre/), it worked rather well for
some of my projects with very low sequence similarity.
Peter
On Tue, 5 May 2009 12:08:04 +0300, Anastassis Perrakis a.perra...@nki.nl
wrote:
Modeller is indeed an excellent program (so are some others) but,
without
Hi,
With 20% identity the main problem is the sequence alignment. Usually
programs that based only sequence data are not enough in such cases
and you need to add additional terms to get the correct structure
(e.g. threading). You can see list of such programs in our site
I think the problem is not in uniqueify but in the GUI implementation.
to run uniqueify you need this sort of information
SYMM P212121
CELL 10 20 30 90 90 90
RESO 2.3
The GUI helpfully tries to extract the information from an existing
reflection file and obviously can get it wrong..
You
I have tried starting idiffdisp from ccp4i, but got a wish window open and a
message saying:
Impossible to load Diffraction Image library
/home/james/build/ccp4-6.1.1/lib/libDiffractionImage.so!! ...
The file is there, though:
ls -l $CCP4_LIB
. . . . . . . . .
. . . .
I am working on a membrane protein. There was problem with the normal
purification of the protein so I have tired to purify it under denaturing
conditions (Using 8M Urea). Luckily I could purify the protein in large
quantity. But now the problem is that I am not able to refold the protein by
step
Urea can modify your protein. Maybe you should also try guanidine HCl. Also,
did you try any detergents? Good luck! Jan
--- Sanjiv Kumar sanjivi...@gmail.com schrieb am Di, 5.5.2009:
Von: Sanjiv Kumar sanjivi...@gmail.com
Betreff: [ccp4bb] Refolding of Denatured Protein
An: CCP4BB@JISCMAIL.AC.UK
My protein mainly has alpha helices and very few beta barrel as predicted by
PSIPRED (http://bioinf.cs.ucl.ac.uk/psipred/psiform.html). There are no
literature available on this protein so I can not be very sure. I have not
tried purifying this protein either with detergent or with *Guanidine
Sanjiv Kumar wrote:
I am working on a membrane protein. There was problem with the normal
purification of the protein so I have tired to purify it under
denaturing conditions (Using 8M Urea). Luckily I could purify the
protein in large quantity. But now the problem is that I am not able
to
Sanjiv Kumar wrote:
I have not tried purifying this protein either with detergent or with
/Guanidine Hydrochloride. I can try with both /Guanidine HCl and
detergent. Since I got good purification with the 8M urea, I was
thinking if this protein could be refolded and used further. Isn't
This protein does not have any trans membrane helices, as predicted by TMHMM
server (http://www.cbs.dtu.dk/services/TMHMM/). Protein is predicted to be
outside the cell by TMHMM. This protein is not there in the soluble
fraction, but it is in the cell pellet. I will try purification with the
Yes, it could be the reason that protein concentration is high. The SDS-PAGE
shows big blob of purified protein of probable size. I can try rapid
dilution method.
Since it is in 8M Urea I have not estimated it yet by any protein estimation
assay, but I am sure that protein concentration is high.
Have a look at REFOLD: http://refold.med.monash.edu.au/
cheers
Ashley
On 05/05/2009, at 9:27 PM, Sanjiv Kumar wrote:
I am working on a membrane protein. There was problem with the
normal purification of the protein so I have tired to purify it
under denaturing conditions (Using 8M Urea).
Preferred Qualifications
This position requires a BA or BS in Chemistry, Biochemistry, or other
related major with at least 5 years of molecular biology or biochemistry
experience, or MS degree in a relevant area plus typically a minimum of 3
years relevant experience. Experience with
It doesn't work outside the GIU either.
I should tell that I have my CCP4 install compiled from source, it is not a
binary installation.
Also that I use ActiveTcl 8.4 and my Linux platform is Ubuntu 8 (64 bit). I
wonder whether
this is a Tcl version issue...
J
Dr James Foadi PhD
Membrane
Hi all,
during concentrating my protein, using Amicon Ultra centrifugal filter devices,
5000g, 4C, I lost large amount of my protein (75%). I heard the same story from
one of my colleagues too. It seems the membrane of the Amicon tube ate my
protein.
Why this happen and how to recover my
Hi,
assuming that 1) you used the right MW cut-off and 2) the membrane is
intact, you probably pelleted your protein onto the membrane.
This often happens if the protein has a limited solubility in the buffer
you are using.
Remember, while concentrating your protein, you are actually
Check the speed--for the 15mL devices, ~3000 x g is the cutoff, I think. You
may be breaking the membranes, and your protein is simply in the bottom of the
concentrator.
JPK
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training
For those of you who have been experiencing my same problem, I have solved it.
It just sufficed downloading and installing the patch (source code bit):
http://www.ccp4.ac.uk/updates/
The compilation went too fast for me to be able to read quickly through the
lines, but I could see
Hi Yanming,
you can try adding 1 M of urea, 1% detergent (OG,DM) that often helps to keep
proteins in solution.
Best wishes
Kornelius
On Tue, 5 May 2009 09:06:09 -0700
yanming Zhang shanma...@yahoo.com wrote:
Hi all,
during concentrating my protein, using Amicon Ultra centrifugal filter
Hello All:
I would like to know if anyone has or knows how to gte this Ecoli strain which
proved to be good for periplasmic protein expression. Ecoli K12 SB 536.
If not, which other strain is good for that?
Thannks Much
Dr. R. Depetris
Weill Cornell Medical College
Hi Yanming,
I usually keep the follow through before I know nothing is in it. Also
you may want to suspend your protein solution every 5-10 min to avoid
precipitation because the concentration gradient forms rapidly during
centrifugation. If all of these do not help, just try concentrators
Hi,
I am looking to have a model produced from a PDB, i.e. something that we
can put on the desk for everyone to admire :)
Googling for such a thing is rather challenging, so I'm curious if anyone
has suggestions as to where I might get something like that made. So far,
I have found two
Chris,
For the laser-etched glass blocks have a look at:
http://www.bathsheba.com/
I have a couple of them and they look very good.
Cheers,
Carsten
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Christopher Rife
Sent: Tuesday,
5-May-2009 22:00 Rehovot
Dear Chris,
See the the page A Physical Model of the β2-Adrenergic Receptor
in Proteopedia at:
http://www.proteopedia.org/wiki/index.php/A_Physical_Model_of_the_β2-Adrenergic_Recepto
r
You can get these kind of models from the MSOE Center for
BioMolecular
I've seen some very pretty 3D models in optical crystal glass made
and sold by
http://www.luminorum.com/
Cheers,
Raji
Disclaimer: I have nothing to do with this company.
On May 5, 2009, at 2:41 PM, Christopher Rife wrote:
Hi,
I am looking to have a model produced from a PDB, i.e.
Hi.
I have experienced similar problems with the Amicon filters previously. I
found that using a swing bucket rather than a fixed angle centrifuge and
keeping the speed at 4000 g, the recommended speed, resulted in better
yields. If you have a large volume to concentrate (12 mL), using an
There's also:
http://bioetch.com/
-Chris
Raji Edayathumangalam wrote:
I've seen some very pretty 3D models in optical crystal glass made and
sold by
http://www.luminorum.com/
Cheers,
Raji
Disclaimer: I have nothing to do with this company.
On May 5, 2009, at 2:41 PM, Christopher Rife
Just buy this cheapo little printer and make your own.
http://www.rap-man.com/
Andreas
Christopher Rife wrote:
Hi,
I am looking to have a model produced from a PDB, i.e. something that we
can put on the desk for everyone to admire :)
Googling for such a thing is rather challenging, so
And another DIY version,
http://homemade3dprinter.blogspot.com/
m
From: docandr...@gmail.com
Subject: Re: [ccp4bb] desktop models
Just buy this cheapo little printer and make your own.
http://www.rap-man.com/
Andreas
Christopher Rife wrote:
Hi,
I am looking to have a model
When using spin concentrators, always remember to not spin more than 4-6min
before remixing the content of the concentrator by pippetting, to prevent
concentration gradient and subsequent precipitation at the bottom.
Jan
Jan K Jensen, Pl-R, Ph.D.
Post doctoral fellow at University of Illinois
On 12:08 Tue 05 May , Anastassis Perrakis wrote:
Modeller is indeed an excellent program (so are some others) but,
without being an expert, I was told some time ago and I am still under
the impression, that homology modeling with 20% identity (and many
insertions and deletions as you
Hi everyone,
It seems that our lab has experienced issues with precipitation of some
proteins (not all) with the Amicon concentrators. For those, we have started
using VivaSpin concentrators. That seems to work fairly well with those that
have issues with the filters. You may want to give it a
Dear Zhang,
Perhaps you can try to concentrate your protein using PEG2.
Put your protein into dialysis tubing and bury it with PEG2. You should
check it every 30-60 min.
Sincerely,
Li
Hi all,
during concentrating my protein, using Amicon Ultra centrifugal filter
sophia
i dont have any idea abt vivaspin concentrators,can u send some details abt
it,sice we are also facing the precipitation problem during the concn.
thanks
atul
-Original Message-
From: CCP4 bulletin board on behalf of Sophia Tsai
Sent: Wed 5/6/2009 7:12 AM
To:
now i have transformed pqe 30 clone into the m15 host successfully, can someone
let me know exactly what was reason behind the problem into transformation??is
it leaky expression into the other host that is toxic for the cells,if it so
then will i would be able to get good expression into
dear sanjiv
i dont think that the removal of detergent is more difficult than urea,since u
are purifying ur protein over Ni-NTA column,so after a few wash over there u
can remove the detergent completely.
best
atul kumar
-Original Message-
From: CCP4 bulletin board on behalf of David
I also some times seen that proteins are not sticking that much with
vivaspin concentrrtors. These are transparent concentrators and it is easy
to collect the concentrated protein by giving an inverted spin for 1
minute. Please check the website for more details www.vivascience.com
Jobi
On
40 matches
Mail list logo
