over cups of tea,
both at Stanford California and in the LMB. His brilliant
scientific mind went hand in hand with his pleasant,civilised,
sometimes funny and immensely interesting persona.
It is never too late to pay respects.
May he rest in peace
Miri
e was no unethical behaviour by either group
> in the
> >> course of their work on these structures and the
> publication of them.
> >>
> >> The problem I am highlighting is that the PDB don't
> understand
>
Sun., June 21st 2015
Good evening,
adding several general points to the thread.
(1) Fundamentally PDB unlike other chemical databases
insists that all equal structures should have the same 3-letter
code and the same atom names - obviously for amino acids and say ATP.
(1.1) Needless to say t
missed.
Miri Hirshberg
Thurs. July 25th, 2013
EBI
also an interesting article on the subject of women in science then and
today
http://www.guardian.co.uk/technology/2013/jul/25/rosalind-franklin-google-doodle
Miri Hirshberg, PDBe
On Thu, 25 Jul 2013, David Schuller wrote:
http://news.cnet.com/8301-1023_3
On Thu, 22 Nov 2012, George T. DeTitta wrote:
Does anyone happen to know if BBC4 broadcasts over the web?
George DeTitta
HWI / UB
bbc.co.uk/iplayer then radio and BBC4
they keep stuff for 7 days
M.
Sent via BlackBerry by AT&T
-Original Message-
From: Martyn Winn
Sender: CCP4 bull
Hirshberg PDBe
On Sat, 22 Sep 2012, Miri Hirshberg wrote:
Sat. Sept. 22nd, 2012
EBI
Good evening,
N-methyl-Pro is a known protein modification.
Was observed in Histone H2B from Drosophila for example. UniProt P02283
indicates that PTM Methylation at Pro-2 increases upon heat shock
The source
are
important.
The best DB for Protein modification is the RESID
http://www.ebi.ac.uk/RESID/
the entry is AA0419
Hope this help
Miri Hirshberg PDBe
p.s. PDB used to have a chem_comp dictionary entry for
this modification, PKR, now obsoleted.
On Sat, 22 Sep 2012, Nicholas M Glykos wrote
Weds., Feb. 15th 2012
EBI
Good evening,
PDB entries with spg P 1- or I -4 C 2 are
3al1 3boi 2gpm 1krl 2gq7 2gq6 2gq5 2gq4 2g32 1pup 3e7r 1vtu 3odv 3trw
3try
you can get information on each from pdbe
pdbe.org/entry
i.e.
pdbe.org/3al1
etc.
Miri, PDBe
On Wed, 15 Feb 2012, Jacob Keller wrote:
Mon. July 4th 2011
EBI
Good evening,
firstly, it could be something that came form the buffer/crystallisation
soup etc. What about phosphate?
Secondly, if you think it is a "natural" post-translation modification of
your specific protein this is gene/source depended. Check the uniprot
entry
inform us of any
other difficulties.
Regards
Miri Hirshberg, PDBe
On Sat, 26 Mar 2011, Daniel Bonsor wrote:
Is the PISA server having problems? I can not seem to upload any structure.
Thanks
Dan
Sun. Oct. 31st, 2010
EBI
Dear Hussey,
there are many paths to take.
Try PDBe (PDB Europe)
http://www.ebi.ac.uk/pdbe-site/pdbemotif/
draw your molecule and search.
Miri - PDBe
Fri. Sept 3rd 2010
EBI
Try ProFit
ttp://www.bioinf.org.uk/software/profit/
as you can give the atom names you want to fit.
Miri
On Fri, 3 Sep 2010, Rex Palmer wrote:
This is not really protein crystallography but we are trying to model build a
ligand into a protein binding site. A
simila
plete list.
click on an entry, and from its atlas page you can get the Quaternary
structure
Miri
On Thu, 29 Jul 2010, Miri Hirshberg wrote:
Thurs., July 29th 2010
EBI
Morning,
I think Andrew meant PDB 2gd1 and 1gd1 (has 4 NAD)
DOI10.1016/0022-2836(88)90130-1
Miri
On Wed, 28 Jul 2010, A Le
Thurs., July 29th 2010
EBI
Morning,
I think Andrew meant PDB 2gd1 and 1gd1 (has 4 NAD)
DOI10.1016/0022-2836(88)90130-1
Miri
On Wed, 28 Jul 2010, A Leslie wrote:
Hi Fred,
If your tetramer show negative cooperativity between the 4 sites for
ligand binding, then it is possible to g
Paul
Dr Miri Hirshberg
European Bioinformatics Institute UK
PDBe - EBI -EMBL
http://www.ebi.ac.uk/pdbe
Phone: +44 (0) 1223 492647
FAX: +44 (0) 1223 494468
Mon., April 5th 2010
EBI
several options with no need for extra software:
(1) goto http://www.ebi.ac.uk/pdbe/
left handside under "Get PDB by ID" enter a pdb idcode for example 1mh1
you get
http://www.ebi.ac.uk/pdbe-srv/view/entry/1mh1/summary
goto Structure primary and click Fasta
cut and past
Mon., April 5th 2010
EBI
several options with no need for extra software:
(1) goto http://www.ebi.ac.uk/pdbe/
left handside under "Get PDB by ID" enter a pdb idcode for example 1mh1
you get
http://www.ebi.ac.uk/pdbe-srv/view/entry/1mh1/summary
goto Structure primary and click Fasta
cut and past
several options with no need for extra software:
(1) goto http://www.ebi.ac.uk/pdbe/
left handside under "Get PDB by ID" enter a pdb idcode for example 1mh1
you get
http://www.ebi.ac.uk/pdbe-srv/view/entry/1mh1/summary
goto Structure primary and click Fasta
cut and paste the sequence
(2) pickup
Fri., Feb. 26th 2010
EBI
Dear all,
I've already replied privately to several people who replied when I first
posted th question, but did not set the record-clear for
the whole community and I do apologize.
What I have is two or more 3D structures, not protein, similar in
their 3D but equival
On Fri, 26 Feb 2010, Liz Potterton wrote:
Miri,
For matching similar small molecules you can try in CCP4mg as described at
http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/superpose.html#interactive_selection
the 'user defined' superposition option with 'monomer' mode. This does 2D
graph isom
Fri., Feb. 26th 2010
EBI
Dear all,
I've already replied privately to several people who replied when I first
posted th question, but did
not set the record-clear for
the whole community and I do apologize.
What I have is two or more 3D structures, not protein, similar in their 3D but
equivalen
linked from www.pdd.org/www.wwpdb.org.
Many thanks to Randy Read, Miri Hirshberg and Kim Henrick for your fast help!
Best regards,
Dirk.
Am 11.02.10 11:19, schrieb Dirk Kostrewa:
Dear Miri,
thanks a lot for looking after this! I would like to have the actual
reference dictionaries for the most
usual compounds. They either have the broken link that I've
mentioned or point to the ftp-site with its cryptic collection.
Anyway, thanks for the pointer.
Best regards,
Dirk.
Am 11.02.10 10:36, schrieb Miri Hirshberg:
Thurs., feb. 11th 2010
EBI
Hello,
to add to Randy Read's note, th
m.ac.uk
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Thurs., Feb. 11th 2010
EBI
----
Dr Miri Hirshberg
European Bioinformatics Institute UK
PDBe - EBI -EMBL
http://www.ebi.ac.uk/pdbe
Phone: +44 (0) 1223 492647
FAX: +44 (0) 1223 494468
Miri Hirshberg
European Bioinformatics Institute UK
PDBe - EBI -EMBL
http://www.ebi.ac.uk/pdbe
Phone: +44 (0) 1223 492647
FAX: +44 (0) 1223 494468
oom 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
pat.l...@drexelmed.edu
----
Dr Miri Hirshberg
European Bioinformatics Institute UK
PDBe - EBI -EMBL
http://www.ebi.ac.uk/pdbe
Phone: +44 (0) 1223 492
based on acive site residues or defined by its volume of cavity with
preferred deviation.
any suggestions could possibly help me.
sincerely
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
--
Dr Miri
Dr Miri Hirshberg
European Bioinformatics Institute UK
http://www.ebi.ac.uk
Phone: +44 (0) 1223 492647
FAX: +44 (0) 1223 494487
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