- "Dima Klenchin" <[EMAIL PROTECTED]> wrote:
> > > 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-h
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Douglas Theobald
Sent: Saturday, December 06, 2008 9:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3D modeling program
- "Dima Klenchin" <[EMAIL PROTECTED]> wrote:
>>>But how do we establ
> 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
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
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
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
to models built on low-homology structures.
since i'm currently preparing my bioinformatics lectures for next week's
teaching, i might as well be a Besserwisser and point out that homology,
much like pregnancy and death, is a binary concept. i'm sure artem knows
this and simply mistyped "low
al Message-
From: Gerard DVD Kleywegt [mailto:[EMAIL PROTECTED]
Sent: Friday, December 05, 2008 3:22 PM
To: Artem Evdokimov
Cc: CCP4 Bulletin Board; Gerard Kleywegt
Subject: Re: [ccp4bb] 3D modeling program
> to models built on low-homology structures.
since i'm currently preparing my bioin
to models built on low-homology structures.
since i'm currently preparing my bioinformatics lectures for next week's
teaching, i might as well be a Besserwisser and point out that homology, much
like pregnancy and death, is a binary concept. i'm sure artem knows this and
simply mistyped "low
ry careful attention must be paid
to models built on low-homology structures.
Good luck,
Artem
_
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of riya
doreen
Sent: Friday, December 05, 2008 12:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] 3D modeling program
Hell
Hello everyone,
I am looking for a modeling program that will allow me to input a sequence
alignment and coordinates of a template for 3D structure prediction of a
target molecule.
I know Modeller can do the job. Are there other web based programs that can
do the same ?
Thanks
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