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:[EMAIL PROTECTED] ****************************************************************** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ******************************************************************
