Hi Reza,
I can recommend the work of Marc-Olivier Coppens and Kourosh Malek and the
references therein for an interesting journey through solvent channels.
David Hargreaves
Associate Principal Scientist
_
AstraZeneca
Discovery S
Sorry for the delayed response -
The situation of 'normal' drug-lead molecule, no restriction of solvent
channel access, no other hindrance to mobility, and rapid on-rates
and/or/with a low Kd driving/maintaining the concentration gradient might be
considered almost optimal. But let us assume th
On 27/06/14 12:00, Reza Khayat wrote:
Hi,
I'd like to do some soaking experiments with a relatively large molecule. Can
someone suggest a program/method to display the solvent channels of a
crystal? We have the crystal structure. I'd like to see if the channels are
large
enough to allow the mol
ferent Kds are in separate figures eg 3-40.
Cheers, BR
Dale Tronrud
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Keller, Jacob
> Sent: Friday, June 27, 2014 3:07 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [cc
You can use CAVER but you would have to make all the symmetry mates as one
chain in order to fool it. Still better to just do the experiment I think.
Either it will work or it won't, regardless of what any software tells you.
Just a wild idea : )
On Fri, Jun 27, 2014 at 5:06 PM, Yarrow Madrona w
Of
> Keller, Jacob
> Sent: Friday, June 27, 2014 3:07 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Solvent channels
>
> And yet halides--even iodide--permeate those same lysozyme crystals and
> others entirely in <30--60 sec.
>
> JPK
>
> -O
Sent: Friday, June 27, 2014 3:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Solvent channels
And yet halides--even iodide--permeate those same lysozyme crystals and
others entirely in <30--60 sec.
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC
ect: Re: [ccp4bb] Solvent channels
Just a remark: diffusion is a slow and random-walk process. Particularly large
molecules in viscous media (PEG anybody?) move (diffuse) slowly in solution. To
simply extrapolate from the fact that the ligand is smaller than the solvent
channels to the odds of
- and you are the easiest person to fool.
R. Feynman, 1974
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Boaz
Shaanan
Sent: Friday, June 27, 2014 2:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Solvent channels
Hi,
I'm not aware of
Hi,
I'm not aware of a program with an option to display channels in crystals but
if you use any of the currently available molecular display program and ask to
display symmetry-related molecules + adjacent unit cells, it should give you a
good enough idea of the spaces between molecules. Using
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