Re: [ccp4bb] 3D modeling program

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: 3D modeling program
From: Douglas Theobald dtheobald {- at -} BRANDEIS {- dot -} EDU
Date: 2008-12-11

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Subject: Re: 3D modeling program
From: Dima Klenchin klenchin {- at -} FACSTAFF {- dot -} WISC {- dot -} EDU
Date: 2008-12-11

Subject: Re: 3D modeling program
From: Douglas Theobald dtheobald {- at -} BRANDEIS {- dot -} EDU
Date: 2008-12-11

----- "Dima Klenchin" 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. (*)
>
> 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 homologous at one level but not at
another. It's also possible for two proteins that have no detectable
similarity above random sequences to be homologous. Hence there is
no circularity.

> "Lets not use generic definition; instead, lets use a specialized
> definition; and lets not notice that the specialized definition wholly
> depends on a system that is built using the generic definition to
> begin with".
>
> Plus, presumably all living things trace their ancestry to the
> primordial soup - so the presence or a lack of ancestry is just a
> matter of how deeply one is willing to look.

This is also wrong. Even if all organisms trace back to one common
ancestor, that does not mean all proteins are homologous. New protein
coding genes can and do arise independently, and hence they are not
homologous to any other existing proteins. You also ignore the levels
of homology concept -- just because two proteins are homologous at one
level does not mean they are homologous at others. For example,
consider these three TIM barrel proteins: human IMPDH, hamster IMPDH,
and chicken triose phosphate isomerase. They are all three homologous as
TIM barrels. However, they are not all homologous as dehydrogenases --
only the human and hamster proteins are homologous as dehydrogenases.

> In other words, it's nice and dandy to have theoretical binary concept
> but in practice it is just as fuzzy as anything else.
>
> IMHO, the phylogenetic concept of homology in biology does not buy you
> much of anything useful. It seems to be just a leftover from
> pre-Darwinian days - redefined since but still lacking solid
> foundation.
>
> Dima

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: 3D modeling program
From: Douglas Theobald dtheobald {- at -} BRANDEIS {- dot -} EDU
Date: 2008-12-11

Next message:
Subject: Re: 3D modeling program
From: Dima Klenchin klenchin {- at -} FACSTAFF {- dot -} WISC {- dot -} EDU
Date: 2008-12-11