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?
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..
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 Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada