Exact motif switch:
The SAAMCO program will return different sets of
matches depending on whether this option is selected or
not.
Exact motif checked:
All amino acids denoted as uppercase within the motif definition
will be matched to. This leads to a smaller search and more specific
results that are relevant if the motif is of known function,
for example.
NOTE:
SAAMCO does NOT match glycine or alanine residues
due to their simplicity, nor does it match proline because of
its cyclical side chain. Therefore these residues will be
replaced with lowercase in a motif definition when the
"Exact motif only" switch is set, or else no matches would
be possible.
Exact motif not checked:
Any combination of 2 or more amino acids within the set of
uppercase residues in the motif definition will
be searched for matches. This will typically lead to more
matches.
Example: (1 motif-protein pair)
LFrmednF 2abc_A
If exact motif is checked, then compounds containing L and
at least two F substituents will be selected and the best
RMSD for superposition of the L, F and F substituents of the
compound on the corresponding protein residues will be calculated.
If exact motif is not checked, then the sequences LF, L......F,
.F.....F and LF.....F will be matched from the compound database.
This second option is useful if there is no information about
which residues are important. In the example above, if the input
text is
LFRMEDNF 2abc_A
i.e. the motif definition defines the complete sequence LFRMEDNF as
matchable, then using a non-exact search allows the user to find any
compounds that match 2 or more subsequences within that sequence.
The number of subsequences increases exponentially with the
total number of non-wildcard residues in the motif definition
,
so it is recommended to restrict the total length of the sequence
when the "Exact motifs only" is not checked.