Folks,
This discussion is now dangerously close to a philosophical discourse
regarding the differences between homoplasy, homology, and analogy. Throw
into the mix synapomorphy and symplesiomorphy - and we've got ourselves a
cladistic analysis soup sprinkled with the croutons of phylogeny.
I do n
> But how do we establish phylogeny? - Based on simple similarity!
> (Structural/morphological in early days and largely on sequence
> identity today). It's clearly a circular logic:
Hardly. Two sequences can be similar and non-homologous at all levels.
Also, two similar proteins can be homologo
- "Dima Klenchin" <[EMAIL PROTECTED]> wrote:
> >Having a generic dictionary definition is nice and dandy. However, in
> >the present context, the term 'homology' has a much more specific
> >meaning: it pertains to the having (or not) of a common ancestor.
> >Thus, it is a binary concept. (*)
>
- "Anastassis Perrakis" <[EMAIL PROTECTED]> wrote:
> I think we are getting a bit too philosophical on a matter which is
> mainly terminology .
>
> 1. To quantify how similar two proteins are, one should best refer to
>
> 'percent identity'. Thats clear, correct and unambiguous.
> 2. One
- "Dima Klenchin" <[EMAIL PROTECTED]> wrote:
>>>But how do we establish phylogeny? - Based on simple similarity!
This is a common, but erroneous, misconception. Modern phylogenetic
methods (Bayesian, maximum likelihood, and some distance-based) rely on
explicit models of molecular evolution,
But how do we establish phylogeny? - Based on simple similarity!
ah! the old rhetorical trick of changing the problem or question a
posteriori! all i pointed out was that things can't be "25% homologous"
Well, you were right that in today's definition things can't be. But you
seem to be miss
We have used Nanodrop for several years and found the readings are always
accurate. The highest concentration we have measured is around 30 mg/ml. The
differences between diluted and concentrated samples are within dilution
error. Nanodrop spectra at low concentration are noisier. We actually prefe
But how do we establish phylogeny? - Based on simple similarity!
ah! the old rhetorical trick of changing the problem or question a posteriori!
all i pointed out was that things can't be "25% homologous" (well, i can think
of a contrived example in which two four-domain proteins have one homol
I agree with previous posts that the reality of inferring evolutionary
relationships is often messy, but there is no excuse for being unclear
on the concepts and, in particular, for use of the % homology construct,
still far too common in supposedly good journals.
BTW, %identity is clear but not a
I think we are getting a bit too philosophical on a matter which is
mainly terminology .
1. To quantify how similar two proteins are, one should best refer to
'percent identity'. Thats clear, correct and unambiguous.
2. One can also refer to "similarity". In that case it should be
clari
Having a generic dictionary definition is nice and dandy. However, in the
present context, the term 'homology' has a much more specific meaning: it
pertains to the having (or not) of a common ancestor. Thus, it is a binary
concept. (*)
But how do we establish phylogeny? - Based on simple simil
Any quotes from Mr Vader about his 7th cousin 15 times removed? phx.
Gerard DVD Kleywegt wrote:
Having a generic dictionary definition is nice and dandy. However, in
the present context, the term 'homology' has a much more specific
meaning: it pertains to the having (or not) of a common anc
I suspect everyone is refering to Rost's "twilight zone" in sequence
similarity where homology modeling trials had better be avoided.
If so, the "twilight zone" would rather correspond to any indefinite
or transitional condition(s) with no applicable or ever relevant binary
constraint(s).
actual
In addition to the possible problem Ho mentioned (DNA conformational
changes), a few other things could effect how doable it is: percentage
of DNA vs protein in the complex and the resolution of the data.
Too little DNA mass wouldn't help phase the remainder of the complex, if
it could be located.
I agree with Gerard regarding "homology", but then it becomes significantly
more problematic when you deal with "remote homology".
Nadir Mrabet
--
Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
INSERM U-724
UHP - Nancy 1, School of Medicine
54505 Vandoeuvre-les-Nancy Cedex
France
Tel : +
I suspect everyone is refering to Rost's "twilight zone" in sequence
similarity where homology modeling trials had better be avoided.
If so, the "twilight zone" would rather correspond to any indefinite
or transitional condition(s) with no applicable or ever relevant binary
constraint(s).
Nadir Mr
Debajyoti Dutta schrieb:
Dear members,
I have a little query hare about Rpim and Rmeans. How these are used to
mark data quality, and how can one calculate it.
Thak you for your reply in advance.
Sincerely
Deb
check out the "R-factors" article in CCP4 wiki at
http://strucbio.biologie
Dear Sir,
Thank you for such nice replies. All of them helped me a lot.
Sincerely
Deb
On Sat, 06 Dec 2008 Manfred S.Weiss wrote :
>
>Dear Deb,
>
>R_meas or R_rim is a merging R-factor which is independent of the
>redundancy or multiplicity of the data (hence its name), R_pim
>stands for prec
Having a generic dictionary definition is nice and dandy. However, in the
present context, the term 'homology' has a much more specific meaning: it
pertains to the having (or not) of a common ancestor. Thus, it is a binary
concept. (*)
A useful paper about homology and percentage sequence iden
Ian Tickle schrieb:
I go along with all Eckhard's cautionary advice & particularly his
suggestion that all restraint info be deposited, as without that it's
impossible to reproduce the experiment! - the restraint info (both
target values & weights or s.d.'s) is literally just as important as the
I go along with all Eckhard's cautionary advice & particularly his
suggestion that all restraint info be deposited, as without that it's
impossible to reproduce the experiment! - the restraint info (both
target values & weights or s.d.'s) is literally just as important as the
X-ray data. The only
Hi Huiying,
I would be very careful to play around with the overall weights for your
purpose. Keep in mind that the overall weights will affect the full
model. Usually the weights on proteins will be well balanced between the
different types of restraints, and you will be meddling with this
ba
Hi,
really strange, I always dilute my protein when taking an absorption
spectra. I try to adjust my expected concentration to a readout of ~
0.2-0.3 OD280. And the Bradford is just as well as 'picking house
numbers', depending on your protein, you can underestimate your
protein concentra
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