Quick Matrix Method

If you lack quantitative affinities but have a consensus sequence or other qualitative information, this program will make a simple matrix for searching Scansite. Write in one or more strongly favored residues in the top row positions in this form. If you know some secondary binding preferences, place those residues in the second row. (A fixed residue is required at position 0, which is why no secondary preference is allowed at that position.)

You can group residues with the wildcards below. If none of them describe the grouping you want, make your own group by separating the residues at one position with slashes, such as "D/E/S/T".

Wildcards:
$ Aliphatic residues (GAVILM)
! Polar uncharged residues (STNQ)
# Positive residues (HKR)
& Negative residues (DE)
@ Aromatic residues (FYW)
X Any residue

Motif Name:


Enter preferred residues here in single-letter amino acid code.
PRIMARY
PREFERENCE
-7
-6
-5
-4
-3
-2
-1
0
+1
+2
+3
+4
+5
+6
+7

Enter secondary preferences in this row.
SECONDARY
PREFERENCE
-7
-6
-5
-4
-3
-2
-1
0
+1
+2
+3
+4
+5
+6
+7

Press Submit when finished. Additional search options will then be presented.



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