SeSAW is a service for locating sequentially and structrally similar motifs to a query protein by searching the Protein Data Bank. In this document we list existing on-line resources relating to SeSAW.
This PDF file briefly describes the SeSAW method and its usage.
This Proteins article describes the dereivation of the SeSAW score and its application to analysis of structural genomics targets. Note that several details of the method (the use of PSI-PRED PSSMs, annotated alignments), as well as the web interface itself were developed after publication of this article.
The application to homology models is described in this conference proceedings.
SeSAW combined with homology modeling has recently been used to study proteins involved in the innate immune response. In this Nature Letter we describe the characterization of zc3h12a, an RNase that is essential for modulating mRNA levels of infammatory cytokines. In this JEM article we demonstrate Tyr kinase activity in ROP16, a Toxoplasma gondii kinase that phosphorylates human Stat3.
SeSAW makes use of several external resources. The program Protein Domain Parser is used to break the query into structural domains. The PSI-BLAST program is used to generate position specific scoring matrices (PSSMs) for both the query and templates from the Uniprot90 representative sequence set. The structural alignment program ASH is used to generate structure neighbors for query and template, as well as to compute structural superpositions. The applet version of the molecular viewer jV is used to display superpositions. The applet version of the alignment editor Jalview is used to display annotated structural alignments.