How do I make a matrix to use in Scansite?
To use your own binding motif in a database search, you will need to define it in a text file and import the text file into Scansite. The format is a matrix of typically 20 columns and 15 rows. The columns are scores for the 20 amino acids at each position, and the 15 rows are positions of each residue in the binding pocket. Scansite requires one residue to be invariant in the motif sequence, such as a tyrosine for motifs recognized by tyrosine-kinases. (For motifs that recognize more than one residue in this position, such as kinases that phosphorylate both serine and threonine, multiple residues can be treated as equivalent in the fixed position.) The middle position, row 8, holds the fixed residue in the matrix. Rows 1 through 7 hold the scores for positions to the left (N-terminal side) of the fixed position, and rows 9 through 15 hold the scores for those to the right (C-terminal) side. Finally, at the top of this 20 by 15 matrix should be a row of column headings indicating the o
