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CCP4BB  December 2008

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Subject:

Re: 3D modeling program

From:

Gerard DVD Kleywegt <[log in to unmask]>

Reply-To:

Gerard DVD Kleywegt <[log in to unmask]>

Date:

Sat, 6 Dec 2008 19:05:34 +0100

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (35 lines)

> 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).

actually, it was russ doolittle who coined the term "twilight zone". burkhard 
rost added the concept of the "midnight zone".

from some of the off-list mails i've been getting some people seem to be 
confused by the fact that establishing the probability of common ancestry of 
two proteins/domains (based on structure and sequence comparison, for 
instance) can be very difficult, and that there may be varying degrees of 
evidence for or against a common ancestry hypothesis. however, this does not 
change the fact that they either do or do not have a common ancestor.

i also realised that the simile between homology and pregnancy can be 
extended: in both cases you sometimes have to worry about xenology -the 
possibility that lateral gene transfer has taken place- see
http://www.massey.ac.nz/~kbirks/gender/whosdad.htm

--dvd

******************************************************************
                         Gerard J.  Kleywegt
     [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                 Biomedical Centre  Box 596
                 SE-751 24 Uppsala  SWEDEN

     http://xray.bmc.uu.se/gerard/  mailto:[log in to unmask]
******************************************************************
    The opinions in this message are fictional.  Any similarity
    to actual opinions, living or dead, is purely coincidental.
******************************************************************

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