BLUE STAR STING Quick Learn

Modes

There are 3 different modes available to the user of STING Millennium. First one is described under the "Initialize STING Millennium" Quick Learn title. That mode simple takes either PDB structure file or PDB formatted model structure and displays it in STING Millennium integrated environment. The other two modes deal with the multiple structure and multiple sequence alignments in a very specific way;

Multiple Structure Alignment with sequences

This STING Millennium mode is allowing the user to view previously aligned structures and then perform variety of analyses on aligned ensemble. Sting Millennium is now capable of using output from CE and PRISM programs. Both of those actually provide PDB formatted file where two aligned structures are placed in a single file (two structures are separated by TER line in PDB). Sequences are provided in a Multiple Sequence Alignment format. However, MSA follows 3D alignment rather than the sequence alignment. In this case, Sequence Window is showing the sequence alignment which obeys the structure alignment, and not just two independent sequences. On the LEFT image, we indicate the path which should be followed by the user in order to get STING presentation of the two aligned structures. Example of the two required files (*.msa and *.pdb) is provided. Save these two files on your computer and then follow the instructions on both left and right image. Resulting presentation shows two amylases structures that are aligned and their sequences ordered in such fashion so that it reflects structural alignment.
The final image here shows how user can paint the amino acids according to the entropy calculated from the differences in two sequences. As there are only two available states (equal and non-equal) entropy has values Zero and One. Consequently, there are only two colors: red and blue, respectively, that indicate those two values. In case of more than 2 structures in the alignment, entropy will have spectrum of (values) colors.