Skip to main content
. 2003 Jul 1;31(13):3328–3332. doi: 10.1093/nar/gkg564

Figure 1.

Figure 1

Figure 1

3matrix visualization of the block query IPB001254A, a serine protease sequence alignment block. The ematrix built from this block is found and displayed here in PDB ID 1AFE, the crystal structure of human thrombin complexed with an inhibitor. (A) The main 3matrix visualization window. The lower right structure display window displays the 1AFE structure with the ‘spacefilling’ option selected for the conserved residues in the scoring matrix, with the blue shading determined by conservation strength. The top of the page contains summary information about the sequence motif, as well as links to the PDB and BLOCKS+ database. The panels on the left of the structure allow the user to display and manipulate the structure display in a variety of ways. (B) The control window for the IPB001254A window. Selecting the ‘all structures’ link in the main 3matrix window opens this window, which lists all PDB structures and chains containing significant matches with ematrixes built from this block. Selecting any of these structures loads it back into the main display window with the sequence motif highlighted in it.