modeller users:
Question 1:
What is considered to be the minimum length of a sequence motif
necessary to derive meaningful constraints from the alignment to use in
modeling.. one, two, three, or more?
i.e.
template -K- -YI- -EEE- -YSIG- -DIDAP-
target -x- -xx- -xxx- -xxxx- -xxxxx-
The Modeller routines tend to pick out longer motifs than Meme,
Matchbox, PIMA, BLOCKS, etc. Smallest motif I have had picked out for
my sequences using these alternative methods is three a.a.'s...
what would be the effect of only matching two, or even just one residue
on the modeling?
which brings me to my next query..
Question 2:
how rigorous must one be with the alignment?
given an template of, say, IPSDC would it be okay to match VPGCC, etc..
trying, in general, to keep acidic matched to acidic, basic to basic,
rings to rings and hydrophobic to hydrophobic, bulky to small, as shown
in (A)..
is this the right method - be less worried about the *exact* nature of
the match, as long as they are physically/chemically similar.. else, is
it best to mix and match among templates, as illustrated in (B)
(A) is this acceptable?
template 1 LPSDC
template 2 VQSAC
template 3 IPSEC
template 4 VPGCC
target IPSDC
(B) or should I break it up like this?
template 1 L-P-S-D-C
template 2 V--QS--AC
template 3 -IP-S--EC
template 4 V-P--G-CC
target -IP-S-D-C
I believe that this is the critical step in the whole procedure, so
your comments would be greatly appreciated!
Nick
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Nick Glover
Department of Chemistry
Simon Fraser University
8888 University Drive
Burnaby, BC
V5A 1S6
Canada