Dear Mahesh,
Instead of bothering with the secondary structure assignments why may
try to superpose your structures and then view your RMSD
plots(Superpose program in CCP4 can do the trick). You might then be
better off focusing on the regions with high RMSD.
Regards
On Sat, Oct 19, 2013 at 3:20
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Dear Mahesh,
In addition to RMSD plots, you could try to quantitatively analyse the
protein residue flexibility in order to detect backbone conformational
transitions by means of the method proposed in:
Local Fluctuations and Conformational Transitions in Proteins
Rocco Caliandro, Giulia
Dear Mahesh,
You could also run the CCP4 program CONTACT/ACT (Tadeusz Skarzynski Andrew
Leslie/Wojtek Rypniewski Howard Terry) for inter residue contacts and compare
the NH-OC bonds in the different structures.
Best,
D
-Original Message-
From: CCP4 bulletin board
Hello experts
Thanks for your insights.
For one of the structures, it turned out to be a rendering issue by pymol
like matt pointed out. For the other, the residues are clearly in a less
than ideal position. Even if I see deviation from the RMSD plots, i cannot
be sure that the structure were
As a postscript it might be worth mentioning one problematic ligand that
suggested to me a way to correct some of the errors mentioned in this thread
R12 is indicated as 9-(4-HYDROXY-2,6-DIMETHYL-PHENYL)-3 in the most recent
Coot monomer library. But in the PDB ligand description it is
Dear Mahesh,
Are all the structures at similar resolution? Definition of secondary
structure is, and can be, affected by the level of geometric
restraints/constraints used in the refinement process.
Tony.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome
Being of an untrusting disposition, I would ask your collaborator for
the reflection data as well as the PDBs - it is always a good idea to
look at the maps when there is some unexpected structural feature! -
The DB provides an electron density server, if the structures have
been deposited,
I dont know about LLG scores - they seem extremely variable depending
on the degree of sequence similarity you assign.
However when you get an R/Rfree of 40%/47% that is a pretty good sign
that at least something is correct.
It isnt clear whether that is after you have placed 2 copies of the
Hi Eleanor,
Yes, the initial LLG scores in Phaser are highly dependent on the assigned
sequence identity, which is translated into an initial estimate of the
effective RMSD of the model. However, the latest versions of Phaser refine the
RMSD estimate at the end of the job and, assuming that
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Sweden
*A postdoctoral research positions is available from the beginning of 2014
in the biomolecular dynamics group of Dr. Gergely Katona at the Department
of Chemistry and Molecular Biology, University of Gothenburg, Sweden.
I guess my experience is out of date - please ignore comments on LLG!
Eleanor
On 21 October 2013 15:40, Randy Read rj...@cam.ac.uk wrote:
Hi Eleanor,
Yes, the initial LLG scores in Phaser are highly dependent on the assigned
sequence identity, which is translated into an initial estimate of
Dear All:
I have a general question about protein- protein interactions. I have two
proteins, A and B. A is a disordered protein while B is a well folded protein.
The binding between A and B has been approved by GST-pull down assay
previously. The strange thing is I cannot get them bind if
Dear Dee,
Some proteins with chaperone-like activity (perhaps your B?) can only
bind to partially folded proteins.
Probably A folds to a molten globule structure after 1-2 days. You can
check by spectroscopic techniques (ANS or Trp fluorescence, CD).
Hope that helps.
Cheers,
Clement
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