Dear Judit
Please allow me to apologise for my recent posting on the ccp4 bulletin board
which may well have come across as slighting your own contribution. I had
earlier
made an innocent and good-natured comment on a thread that I felt was
relevant. In fact it seems to me interesting how other f
mous, whether or not we regard
protein
crystallography as a video game where the person with the lowest R-factor wins.
best wishes to all!
Jeremy the Pedant
Begin forwarded message:
> From: Kevin Jude
> Date: February 27, 2015 3:25:24 AM GMT+09:00
> To: Jeremy Tame
> Cc: CCP4B
I think Goodhart's Law applies here (see the Wikipedia page):
When a measure becomes a target, it ceases to be a good measure.
From memory I believe Randy Read and George Sheldrick have commented that
Ramachandran plots are a good measure of structure quality, and therefore should
not be used expl
Dear Hay
I suggest that you use analytical ultracentrifugation to determine the
oligomeric state of the protein in solution.
Mass spectrometry and light scattering are also useful, but there are so many
examples of gel filtration proving
erroneous it has questionable value as an analytical techn
Hi Katherine
I think this topic has been touched on before on CCP4BB. Any rigid body
motion can be decomposed into a single translation and a rotation about
that vector. In the case of a two-domain protein with a flexible hinge, the
translation component is often close to zero and a pure rotation
You may be missing a trick by not using metals as crystallisation additives if
your best
diffraction is only 3.5 Angstroms. Uranium has to be my favourite heavy metal,
even if
I've solved more structures with Pt and Hg. It gave crystals diffracting to 1.2
A from a
protein that otherwise gave no
The best reference by far for the hydrophobic interaction is
Israelachvili's Intermolecular and Surface Forces.
Anyone really interested in the topic will probably also like books by Ninham
such as
Hyde et al, The Language of Shape.
I cannot really recommend the later book
Ninham and Lo Nostro, "
Different proteins do different things. Some adopt fewer conformations and a
more rigid structure after binding
a ligand, and others do the opposite. Haemoglobin is a nice example of a
protein that becomes a lot more flexible
after picking up ligands. For any reaction of the kind P + L -> PL ther
>
>
> On 20 Jun 2012, at 07:34, Jeremy Tame wrote:
>
>> I agree with Petr. For a rigid body displacement the RMSD is not much use as
>> a descriptor. Such
>> a displacement can be described by a translation along and rotation around a
>> direction, or
>
I agree with Petr. For a rigid body displacement the RMSD is not much use as a
descriptor. Such
a displacement can be described by a translation along and rotation around a
direction, or
rotation-translation matrices. These will allow someone else to reproduce the
displacement,
but the RMSD wi
Well it's not as impressive as some solutions posted, but three lines of awk
will
do the job too. Search for END or ENDMDL as you wish.
BEGIN {file = 0; filename = "charlie_" file ".pdb"}
/ENDMDL/ {getline; file ++; filename = "charlie_" file ".pdb"}
{print $0 > filename}
Call this script "char
Several people have already pointed out that a "pull-down" is not
a rigorous, quantitative method. Mackay et al (TIBS 32, 530-531, 2007)
have some interesting comments to the effect that many reported
interactions found by pull-down or immunoprecipitation are simply
artefacts. Pull-downs are also
:
Jeremy Tame
Protein Design Laboratory, Yokohama City University
Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan
Tel +81 (0)45 508 7228Fax +81 (0)45 508 7366
The term T{delta}S is not proportional to temperature however since
entropy is itself a function of T. Thus (for example) the hydrophobic
effect
reaches a maximum at around 25 deg C rather than being a monotonic
function of temperature.
Incidentally human adult Hb (HbA) has a concentration of
When you say you want an easy-to-get-easy-to-use binding energy/contact
area calculator I assume you mean a simple scoring function.
I have suggested that such functions cannot achieve reliable, accurate
general
affinity estimation (pdfs sent separately), and so far this seems to
be borne out (s
15 matches
Mail list logo
