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:

- CCP4BB

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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: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-12-11

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

> > 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.

Of course there is. Just how do you establish that the two are not
homologous? - By finding that they don't belong to the same branch. And how
do you decide what constitutes the same branch? - By looking at how similar
things are!

> > 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.

Just how do they arise independently? Would that be independent of DNA
sequence? And if not, then why can't shared ancestry of the DNA sequence
fully qualify for "homology"?

> 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.

... And all that is concluded based on sequence similarities [of other
proteins/DNAs] to construct phylogenetic tree. So, ultimately, homology ~
similarity.

The "generic" concept of homology used to be used as a proof of evolution.
Today, things seem to be reversed and evolution is being used to infer
homology. A useful concept turned into a statement with little or no utility.

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: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-12-11