Biochemical and Structural Information for Yeast Proteins in SGD.

Contents

PDB Homologs
Motifs
Protein Information
Other Resources at SGD

This page contains supplemental material for the paper describing new protein tools and resources in SGD in the 2003 Nucleic Acids Research database issue (see Weng et al (2003) NAR 31:216-218). All of these tools and resources can be reached from the SGD home page.

PDB Homologs

The PDB homologs page provides a list of all solved structures available in PDB relevant to a given S. cerevisiae protein. SGD locus pages provide links to the PDB results page, and you can also use the PDB Search page to access the PDB results directly.
Useful links:

PDB search
PDB help: Search help | Results help | Alignment help

Motifs

The Motif tool searches for motifs in a particular protein using the eMOTIF resource. SGD locus pages provide links to the Motifs page, and you can also search for motifs directly using the Motif Search page.
Useful links:

Motif search
Motif help
eMOTIF site (described in Huang and Brutlag (2001) NAR 29: 202-204.)

Protein Information

The Protein Information resource contains calculated data based on protein sequence. SGD locus pages provide links to the Protein Information page, and you can also use the Protein Information Search page to access this information directly. All of these data are also available for download via the SGD ftp site.
Useful links:

Other Resources at SGD

Gene Ontology (GO): the Gene Ontology, or GO, is a structured, controlled vocabulary to describe the molecular function, biological process, and cellular component of a gene product. Using GO is a powerful way to search within and across different organism databases, and new tools are being developed to utilize GO in the analysis of genome-wide experimental results.
Useful links:

GO Tutorial: a great interactive overview to using GO at SGD.

GO Help at SGD: more detailed description of GO.

GO Home page: the GO consortium's home page, with links to GO tools, gene product annotations, and more.

ftp site: almost all of the data contained within SGD is available for download on the SGD ftp site. Most of the data can be found in the data_download directory.

Vector db: the Vector db, created by Stephen Misener, is now hosted at SGD. You can search or BLAST for vector sequences from Drosophila, C. elegans, and S. cerevisiae.

SGD searches: on the SGD search page, there are links to search tools for expression data, functional analyses, external databases, and others.

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