Re: [ccp4bb] protein interactions

2012-09-07 Thread LEDU Marie-Helene 161111 
Search for homologous binding partners with close or remote homologies
with your own sequences can also be addressed from the InterEvol database
http://biodev.cea.fr/interevol/
It seems you can upload the sequences there :
http://biodev.cea.fr/interevol/interevalign.aspx

Hope this can help
Marie-Ln


Dr Marie-Hélène LeDu
Laboratoire de Biologie Structurale et Radiobiologie
CEA/DSV/IBiTec-S, CEA Saclay
Bât 144, pièce 25
91191 Gif-sur-Yvette, France
Tel : 33 (0)1 69 08 71 35
E-mail : marie-helene.l...@cea.fr





Le 06/09/12 14:20, « moham...@strubi.ox.ac.uk » 
a écrit :

>Hi Careina,
>
>In answer to your first question you could also try the iPATCH server:
>
>http://portal.stats.ox.ac.uk/userdata/proteins/i-Patch/home.pl
>
>This takes two reference structures for proteins that interact, and
>combined with multiple sequence alignments of their homologs attempts to
>predict the surface contact residues between them.
>
>As far as your second question is concerned, a quick google search using
>the term "protein interaction prediction from sequence" gave some useful
>links, one of which is Struct2Net:
>
>http://groups.csail.mit.edu/cb/struct2net/webserver/
>
>This tool attempts to predict protein-protein interactions purely from
>sequence data. However, it does use a structure-based threading approach,
>so your sequences will be run against the pdb. If they are unique to
>anything in the structural databases, it may not be useful.
>
>
>Hope this helps,
>
>Mohammad
>
>
>
>Dr. Mohammad W. Bahar
>Division of Structural Biology
>Wellcome Trust Centre for Human Genetics
>University of Oxford

[ccp4bb] FW: est-ce que tu peux mettre ça sur CCP4 ?

2011-07-05 Thread LEDU Marie-Helene 161111 


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will be useful. Starting date is from September 2011. A one year funding
that can be extended to three years on a related project is available.

Please submit application and CV  to: sophie.z...@cea.fr
 .


Dr Sophie Zinn-Justin
Laboratoire de Biologie Structurale et Radiobiologie
iBiTec-S, CEA Saclay
91190 Gif-sur-Yvette
 
http://www-dsv.cea.fr/dsv/instituts/institut-de-biologie-et-de-technologies-
de-saclay-ibitec-s/unites/service-de-bioenergetique-biologie-structurale-et-
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[ccp4bb] POSTDOCTORAL POSITION IN PROTEOMICS / CELLULAR BIOLOGY FOCUSED ON THE ROLE OF NUCLEAR LAMINS IN THE RESPONSE TO OXYDATIVE STRESS

2011-01-11 Thread LEDU Marie-Helene 161111 
 

POSTDOCTORAL POSITION IN PROTEOMICS / CELLULAR BIOLOGY FOCUSED ON THE ROLE
OF NUCLEAR LAMINS IN THE RESPONSE TO OXYDATIVE STRESS

 

A new postdoctoral position is becoming available at CEA, a research
institute located in the south-west suburb of Paris. The postdoctoral
project aims at determining essential molecular mechanisms linking genome
spatial organization and genome integrity. It is focused on the elucidation
of the role of nuclear lamins in the response to oxidative stress. It will
be carried out at the interface between two teams of complementary
expertises: (1) the team of Pascale Bertrand, which recently characterized
lamin defaults in cells deficient in DNA damage signalling proteins on the
basis of cell biology experiments and is running a proteomic core facility
to detect partners from 2D gels of complexes; (2) the team of Sophie
Zinn-Justin, which has determined the 3D structures of several nuclear
envelope protein domains as in particular the lamin C-terminal domain and is
now involved in the characterization at the atomic level of interactions
between these domains and their biological partners. Experience in cell
biology and/or biochemistry is essential. The candidate should also be
interested by molecular aspects and biophysics. Competitive salary (2230
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is flexible. 
Interested candidates should forward a Curriculum Vitae, and electronic and
postal addresses of potential references via e-mail: pascale.bertr...@cea.fr
and 
sophie.z...@cea.fr


Dr Sophie Zinn-Justin
CEA/DSV/IBiTec-S
Laboratoire de Biologie Structurale et Radiobiologie
bat 144, CE Saclay
91191 Gif-sur-Yvette
FRANCE
email : sophie.z...@cea.fr
tel: (33) (0)1 69 08 30 26

Re: [ccp4bb] Density peaks to build

2010-07-21 Thread LEDU Marie-Helene 161111 
Dear Fatima,

I have used Buster to refine alternate occupanies at 1.2 A or 1.4 A
resolution, and it greatly improved the electron density as well as the
output statistics.

Best,

Marie-Hélène


Dr Marie-Hélène LeDu
CEA/DSV/IBiTec-S
Laboratoire de Biologie Structurale et Radiobiologie
bat 144, CE Saclay
91191 Gif-sur-Yvette
email : marie-helene.l...@cea.fr
tel:01 69 08 71 35





Le 21/07/10 09:53, « Fatima Fonseca »  a écrit :

> Dear Chris and Leo,
> 
> Thank you for your suggestions.
> 
> I am refining the 1.08 A structure in SHELXL and I have Hs added; I think
> refinement is at a final stage. I did start with the 50%, 25+25% occupancy but
> then I changed to 0.33 each ... I need to refine this further.
> 
> For the 1.35A data, model is complete (except for some C- and N-terminal
> residues) and I've refined alternative conformations too. The crystallization
> condition is Sodium acetate and PEG3350 with ethylene glycol as cryo. I have
> some molecules of cryo and Na in the model. I¹ll try other cat/anions and
> refine.
> 
> Best,
> Fátima

[ccp4bb] trouble with protein storage

2009-11-18 Thread LEDU Marie-Helene 161111 
Hello,

Sorry for the unrelated question.
We encounter important storage problem of our favorite protein. 
We can not freeze it without a lost of 50 to 90 %, and can not use glycerol 
without precipitation. 
Would anybody have suggestions or references that could help us ?
Thanks a lot in advance.

Marie-Helene

Dr Marie-Hélène LeDu
CEA/DSV/IBITEC-S/LBSR
bat 144, CE Saclay
91191 Gif-sur-Yvette
FRANCE
tel 01 69 08 71 35
emel : marie-helene.l...@cea.fr

Re: [ccp4bb] PHASER packing function with DNA

2009-08-06 Thread LEDU Marie-Helene 161111 
Hi,

Thanks a lot for the replies. It seems that Randy¹s solution works fine.

Marie-Ln


Le 6/08/09 13:54, « Randy Read »  a écrit :

> Hi,
> 
> That's actually the last question answered on our FAQ page!
> 
> http://www-structmed.cimr.cam.ac.uk/phaser/faq.html
> 
> Basically, you'll want to change lines like this:
> ATOM  1  PGd C   1  23.560  11.045  11.025  1.00 53.18   P
> to lines like this:
> ATOM  1  P G C   1  23.560  11.045  11.025  1.00 53.18   P
> because Phaser 2.1.4 expects the residue name in one-letter code in column 20.
> 
> We didn't notice, before releasing version 2.1.4, that one effect of the PDB
> remediation was to change the nomenclature for nucleic acid residues, so the
> packing check won't work using files recently obtained from the PDB (where
> deoxy-G is represented as DG in columns 19-20).  This is fixed for version
> 2.2.x (available as part of Phenix nightly builds, and hopefully from an
> upcoming CCP4 release); in the meantime, you'll have to edit recent PDB files
> before running Phaser.
> 
> Best wishes,
> 
> Randy Read
> 
> On 6 Aug 2009, at 11:25, LEDU Marie-Helene 16 wrote:
> 
>>  Dear CCP4BBer,
>>  
>>  I'm using Phaser 2.1.4 to solve a structure containing both protein and DNA.
>> The packing function works find with the protein, but does not recognize the
>> trace of the DNA. Does anyone know precisely what should be the pdb format ?
>>  Here is the format that I'am using :
>>  ATOM  1  PGd C   1  23.560  11.045  11.025  1.00 53.18
>> P  
>>  ATOM  2  OP1  Gd C   1  24.884  10.499  11.417  1.00 54.98
>> O  
>>  ATOM  3  OP2  Gd C   1  22.319  10.778  11.791  1.00 44.44
>> O  
>>  ATOM  4  O5'  Gd C   1  23.716  12.601  10.891  1.00 47.89
>> O  
>>  ATOM  5  C5'  Gd C   1  24.689  13.001   9.945  1.00 42.99
>> C  
>>  ATOM  6  C4'  Gd C   1  24.395  14.391   9.437  1.00 39.27
>> C  
>>  ATOM  7  O4'  Gd C   1  23.172  14.464   8.683  1.00 35.25
>> O  
>>  ATOM  8  C3'  Gd C   1  24.264  15.347  10.617  1.00 36.72
>> C  
>>  ATOM  9  O3'  Gd C   1  25.063  16.487  10.335  1.00 34.52
>> O  
>>  ATOM 10  C2'  Gd C   1  22.807  15.691  10.507  1.00 34.06
>> C  
>>  ATOM 11  C1'  Gd C   1  22.474  15.641   9.080  1.00 27.89
>> C  
>>  ATOM 12  N9   Gd C   1  21.218  15.303   8.921  1.00 20.00
>> N  
>>  ATOM 13  C8   Gd C   1  20.436  14.344   9.523  1.00 20.00
>> C  
>>  ATOM 14  N7   Gd C   1  19.207  14.292   9.056  1.00 20.00
>> N  
>>  ATOM 15  C5   Gd C   1  19.159  15.275   8.076  1.00 20.00
>> C  
>>  ATOM 16  C4   Gd C   1  20.381  15.912   7.978  1.00 20.00
>> C  
>>  ATOM 17  N1   Gd C   1  18.457  16.733   6.390  1.00 20.00
>> N  
>>  ATOM 18  C2   Gd C   1  19.700  17.306   6.353  1.00 20.00
>> C  
>>  ATOM 19  N3   Gd C   1  20.705  16.934   7.129  1.00 20.00
>> N  
>>  ATOM 20  C6   Gd C   1  18.087  15.691   7.242  1.00 20.00
>> C  
>>  ATOM 21  O6   Gd C   1  16.928  15.244   7.199  1.00 20.00
>> O  
>>  ATOM 22  N2   Gd C   1  19.883  18.288   5.476  1.00 20.00
>> N  
>>  
>>  Thanks,
>>  
>>  Marie-Ln
>>  
>>  Laboratoire de Biologie Structurale et Radiobiologie
>>  CEA/DSV/IBiTec-S/SB2SM
>>  bat144, pièce 25
>>  91191 Gif-Sur-Yvette
>>  Tel : 33 (0)1 69 08 71 35
>>  E-mail : marie-helene.l...@cea.fr
>>  -- 
>>  
>>  
>>   
>>   
> 
>  
> --
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research  Tel: + 44 1223 336500
> Wellcome Trust/MRC Building   Fax: + 44 1223 336827
> Hills RoadE-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk
>  
> 
>

[ccp4bb] PHASER packing function with DNA

2009-08-06 Thread LEDU Marie-Helene 161111 
Dear CCP4BBer,

I'm using Phaser 2.1.4 to solve a structure containing both protein and DNA.
The packing function works find with the protein, but does not recognize the
trace of the DNA. Does anyone know precisely what should be the pdb format ?
Here is the format that I'am using :
ATOM  1  PGd C   1  23.560  11.045  11.025  1.00 53.18
P  
ATOM  2  OP1  Gd C   1  24.884  10.499  11.417  1.00 54.98
O  
ATOM  3  OP2  Gd C   1  22.319  10.778  11.791  1.00 44.44
O  
ATOM  4  O5'  Gd C   1  23.716  12.601  10.891  1.00 47.89
O  
ATOM  5  C5'  Gd C   1  24.689  13.001   9.945  1.00 42.99
C  
ATOM  6  C4'  Gd C   1  24.395  14.391   9.437  1.00 39.27
C  
ATOM  7  O4'  Gd C   1  23.172  14.464   8.683  1.00 35.25
O  
ATOM  8  C3'  Gd C   1  24.264  15.347  10.617  1.00 36.72
C  
ATOM  9  O3'  Gd C   1  25.063  16.487  10.335  1.00 34.52
O  
ATOM 10  C2'  Gd C   1  22.807  15.691  10.507  1.00 34.06
C  
ATOM 11  C1'  Gd C   1  22.474  15.641   9.080  1.00 27.89
C  
ATOM 12  N9   Gd C   1  21.218  15.303   8.921  1.00 20.00
N  
ATOM 13  C8   Gd C   1  20.436  14.344   9.523  1.00 20.00
C  
ATOM 14  N7   Gd C   1  19.207  14.292   9.056  1.00 20.00
N  
ATOM 15  C5   Gd C   1  19.159  15.275   8.076  1.00 20.00
C  
ATOM 16  C4   Gd C   1  20.381  15.912   7.978  1.00 20.00
C  
ATOM 17  N1   Gd C   1  18.457  16.733   6.390  1.00 20.00
N  
ATOM 18  C2   Gd C   1  19.700  17.306   6.353  1.00 20.00
C  
ATOM 19  N3   Gd C   1  20.705  16.934   7.129  1.00 20.00
N  
ATOM 20  C6   Gd C   1  18.087  15.691   7.242  1.00 20.00
C  
ATOM 21  O6   Gd C   1  16.928  15.244   7.199  1.00 20.00
O  
ATOM 22  N2   Gd C   1  19.883  18.288   5.476  1.00 20.00
N  

Thanks,

Marie-Ln

Laboratoire de Biologie Structurale et Radiobiologie
CEA/DSV/IBiTec-S/SB2SM
bat144, pièce 25
91191 Gif-Sur-Yvette
Tel : 33 (0)1 69 08 71 35
E-mail : marie-helene.l...@cea.fr
--