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. 2003 Jan 1;31(1):216-8.
doi: 10.1093/nar/gkg054.

Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins

Shuai Weng  1 , Qing Dong, Rama Balakrishnan, Karen Christie, Maria Costanzo, Kara Dolinski, Selina S Dwight, Stacia Engel, Dianna G Fisk, Eurie Hong, Laurie Issel-Tarver, Anand Sethuraman, Chandra Theesfeld, Rey Andrada, Gail Binkley, Christopher Lane, Mark Schroeder, David Botstein, J Michael Cherry
Affiliations

Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins

Shuai Weng et al. Nucleic Acids Res. .

Abstract

The Saccharomyces Genome Database (SGD: http://genome-www.stanford.edu/Saccharomyces/) has recently developed new resources to provide more complete information about proteins from the budding yeast Saccharomyces cerevisiae. The PDB Homologs page provides structural information from the Protein Data Bank (PDB) about yeast proteins and/or their homologs. SGD has also created a resource that utilizes the eMOTIF database for motif information about a given protein. A third new resource is the Protein Information page, which contains protein physical and chemical properties, such as molecular weight and hydropathicity scores, predicted from the translated ORF sequence.

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Figures

Figure 1
Figure 1
Protein structure information at SGD: the new PDB Homologs tool. Due to space considerations, both (A) and (B) are just a portion of the web display. (A) The PDB Homologs results page lists the results of the Smith–Waterman sequence comparison of a S. cerevisiae protein against the proteins in PDB. Links are provided to the PDB and other external protein structure databases, as well as the alignment page shown in B. In this example, Fpr1p results are shown. A structure of the S. cerevisiae was identified (first row in the table), as well as additional structures of the Bos taurus homolog. Additional homologs were found but are not shown. This page can be reached from the ‘Protein Info and Structure’ pull-down menu on Locus and Protein Information pages. (B) The PDB Alignment page displays the alignment of the S. cerevisiae protein and the PDB protein, a color ribbon image of the structure (provided by PDB), and links to other databases and tools such as the interactive structural viewer QuickPDB provided by the PDB.
Figure 1
Figure 1
Protein structure information at SGD: the new PDB Homologs tool. Due to space considerations, both (A) and (B) are just a portion of the web display. (A) The PDB Homologs results page lists the results of the Smith–Waterman sequence comparison of a S. cerevisiae protein against the proteins in PDB. Links are provided to the PDB and other external protein structure databases, as well as the alignment page shown in B. In this example, Fpr1p results are shown. A structure of the S. cerevisiae was identified (first row in the table), as well as additional structures of the Bos taurus homolog. Additional homologs were found but are not shown. This page can be reached from the ‘Protein Info and Structure’ pull-down menu on Locus and Protein Information pages. (B) The PDB Alignment page displays the alignment of the S. cerevisiae protein and the PDB protein, a color ribbon image of the structure (provided by PDB), and links to other databases and tools such as the interactive structural viewer QuickPDB provided by the PDB.
See this image and copyright information in PMC

References

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