Hi Lucas,
you can send your PDB file to this server and get the information you
want in one of their analysis.
http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/upload.html
Jürgen
On 22 Nov 2008, at 14:45, Lucas Bleicher wrote:
By the way, is there a program (perhaps one of those cited on
By the way, is there a program (perhaps one of those cited on this thread) that
would list all salt bridges and hydrogen bonds for residues in the same chain?
Lucas
Veja quais são os assuntos do momento no Yahoo! +Buscados
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Hi Frederic,
Just to add to the list:
PSAIA
http://complex.zesoi.fer.hr/tools/PSAIA.html
GETAREA
http://curie.utmb.edu/getarea.html
and NACCESS
http://www.bioinf.manchester.ac.uk/naccess/
We've used these for calculating polar and apolar contributions to
binding surface areas (in particular
The MolProbity server allows you to look at contacts between two
interfaces. You will see H-bonds, van der Waals interactions, and
steric clashes in a kinemage view, as well as in a text list form if
desired.
You can also use our program 'Probe' offline, which may be dowloaded here:
http://kinem
I also like the http://i.moltalk.org server for interface analysis. On
the website click on "Find Interface between two chains of a structure":
it is very simple to use and the output table lists and describes all
atom-atom contacts between two chains within a chosen cutoff distance.
Oliv
Ele
Vellieux Frederic wrote:
Dear Colleagues,
I am looking for a program (if there is one...) that would allow to
list all interactions at a dimer interface (polar, ie hydrogen bonds
and salt bridges, and non polar).
Thanks in advance for your replies.
Best regards,
Fred.
Have you tried MSDpi
Hi,
Wouldn't ccp4/contacts and the website PISA do that for you ?
Boaz
- Original Message -
From: Vellieux Frederic <[EMAIL PROTECTED]>
Date: Thursday, November 20, 2008 12:29
Subject: [ccp4bb] looking for a program
To: CCP4BB@JISCMAIL.AC.UK
> Dear Colleagues,
>
Dear Colleagues,
I am looking for a program (if there is one...) that would allow to list
all interactions at a dimer interface (polar, ie hydrogen bonds and salt
bridges, and non polar).
Thanks in advance for your replies.
Best regards,
Fred.
begin:vcard
fn:Fred. Vellieux (Ph.D)
n:Vellieux
