Dear all,
Does anyone know a program or web server that can predict Kd value between two
proteins from a solved complex structure?
Regards
Wei
Hi,
PISA have something like this, I think, or at least deltaG estimate.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or
Hi,
As far as I understand the DeltaG given by PISA is kind of a stability
measure of the complex, not its binding DeltaG. It is also based on a
small part of the terms that contribute to a binding energy. I may be
wrong about that, but in any case, predicting a KD from a single
structure is
For the low cost of $10 USD, this should be about as reliable :)
http://www.amazon.com/Mattel-30188-Magic-8-Ball/dp/B1ZWV7
Not trying to be a curmudgeon, but this is a really hard problem!
Steve
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
Don't believe such program/server does exist. Notice that you are asking for
something that *can* predict Kd. One can *try* making such predictions and
they may even be routinely in the ballpark, assuming that you are satisfied
with being routinely off by, say, an order of magnitude.
One
Hi,
You also can try the MR program Queen of Spades (Qs) (
http://utopia.duth.gr/~glykos/Qs.html; documentation,
http://utopia.duth.gr/~glykos/pdf/Qs.pdf). It is a multi-dimensional MR, so
it will use a lot of CPU time and memory, but might be worth try it.
Good luck.
Andrey Nascimento
2013/4/18
Hi Wei,
I'm unsure if this will help, as i've never used it myself, but a former
colleague in France is working on such a server?
http://2p2idb.cnrs-mrs.fr/
But as everyone else has stated, only use this in comparison to some hard
physical data.
Cheers,
Mat
Dear all,
I am trying to refine a beta-D-N-Acetyl glucosamine moiety (NAG) linked
to an asparagine (ASN) in Refmac.
(version CCP4 6.3: Refmac_5.5.0110 version 5.5.0110 : 08/05/10)
The sugar has two alternate conformations that occupy the same position in the
electron
density but are rotated
Hi Markus,
You could try changing your Refmac version. The version you are using is
ancient. You may have an old version in your PATH next to the new one because
your CCP4 seems up to date.
AFAICT there is nothing wrong with the LINKR or the HETATM records
Sent from my Windows Phone
Hi Robbie,
Oops, sorry, I used
CCP4 6.3: Refmac_5.7.0032 version 5.7.0032 : 05/09/12
(confirmed by the log file)
so I am using the current version and the problem still persists.
Thanks!
Markus
On 18/04/13 03:31 PM, Robbie Joosten wrote:
Hi Markus,
You could try changing your Refmac
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