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SGD Help: PDB Homolog Query
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Contents
The PDB Homolog Query page allows you to search for structural information on Saccharomyces cerevisiae proteins. The search will retrieve the "PDB Homolog" page for that yeast protein, if it is available. The PDB Homolog page will list the yeast protein structure (if it has been solved) along with other proteins of known structure that have sequence similarity to the query protein. The PDB Homolog page also provides further links to structural and alignment information for these proteins. Structure infomation is retrieved from the RCSB Protein Data Bank (PDB) and the sequence similarity analysis is performed by the Smith-Waterman algorithm.
There are four different Query Options, listed below. Ultimately,
each option will retrieve a PDB Homolog page for a Saccharomyces
cerevisiae protein, if that information is available. The options
vary in that some have intermediate "retrieved lists" where you can
choose among yeast proteins that have PDB Homologs and also meet the
specified parameters.
- Gene/ORF Name
Enter a Saccharomyces cerevisiae gene or ORF to retrieve a list
of PDB Homolog page for the query yeast gene or ORF name, along with
links to structural and alignment information.
- Keyword
Enter a text keyword to retrieve a list of yeast genes, along
with their respective PDB Homologs, where the keyword has a
match in the "Gene Product" field or "GO annotations" in SGD. The
retrieved list provides further links to the PDB Homolog
pages.
- PDB Identifier
Enter a PDB Identifier to retrieve a list of yeast proteins with
sequence similarity to a protein listed in PDB. The retrieved list
provides further links to the PDB Homolog pages.
- Chromosome
Choosing a Chromosome number retrieves a list of all genes on that
yeast chromosome that have either solved protein structures or
sequence similarity to proteins with solved structures. The retrieved
list provides further links to the PDB homolog pages.
The PDB Homolog Query Page can be accessed by selecting the PDB
Homolog Query link from the SGD Search
Page. Selecting the PBD Homologs link from any SGD locus
page retrieves a list of PDB Homolog page for that gene, if it is
available, along with links to structural and alignment information.
- Links within SGD
- Help for PDB Homologs Results page
- Protein Viewer Resource page
- External links
- PDB
Return to Saccharomyces Genome Database