SeSAW (sequence-derived structural alignment weights) is a web-based program for identifying functionally or evolutionarily conserved motifs in protein structures by locating sequence and structural similarities, and quantifying these at the level of individual residues. Results can be visualized in 2D, as annotated alignments, or in 3D, as structural superpositions. An example is given for both an experimentally determined query structure and a homology model.
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SeSAW: balancing sequence and structural information in protein functional mapping.
Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H.
Bioinformatics. 2010 May 1;26(9):1258-9. Epub 2010 Mar 17.