> 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
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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]
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