HMMSTR-CM is a method for predicting the 2D contact map of a protein from the sequence alone. A contact potential energy map (Eij) like the one below is calculated using HMMSTR contact potentials. Energies for each possible ij contact are displayed using a red-to-blue color scale. A threshhold is chosen and all ij contacts with energy below that cutoff are predicted to be in contact. In practice, a contact map predicted using a simple threshhold is usually not accurate, or even physcially possible. For a description of the succeeding steps in HMMSTR-CM, not carried out by this server, please refer to the following:

Shao Y & Bystroff C. (2003a). Predicting inter-residue contacts using templates and pathways. Proteins, Structure, Function and Genetics 53 Suppl 6:497-502. abstract PDF

Shao Y & Bystroff C. (2003b). Modeling Protein Folding Pathways. Practical Bioinformatics (Bujnicki, J. M., Ed.), Springer-Verlag, Heidelberg. abstract PDF


Each axis is the position in the sequence. The upper triangle shows the contact potential for each pair of positions, colored red for low energy to blue for high energy. ij pairs below a threshhold (defined separately for each sequence separation distance) are outlined in the upper triangle and plotted in the lower triangle.

The bars along the diagonal represent the amino acid type: black bars for non-polar, grey bars for uncharged polar, no bar for charged sidechains, yellow-green bar for glycine.