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Welcome to the Yeast Resource Center Public Data Repository

Search the YRC PDR protein database:

Search examples: protein names, descriptions, SGD IDs, swiss-prot IDs, NCBI GI IDs, uniprot IDs, flybase IDs, etc.

[Advanced Search]
The YRC PDR currently contains 9,678,820 descriptions for 5,530,667 proteins from many databases.

To get started, use the search form above, or the "Quick Search" at the upper-right on any page in the website to search names or descriptions of proteins in our database. For more focused searches, use the Advanced Search page. If you have any questions, comments or suggestions, please use our Feedback page.

The YRC PDR provides access to scientific experimental data resulting from collaborations and technology development involving the Yeast Resource Center. The data has been made public either through publication or by specific consent of the researchers involved. The YRC PDR is described in more detail in the following publication: Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D378-82

Changes & Additions:

August 17, 2011 - The proteome folding project paper has been published. [-Hide Details]

The proteome folding project describing the generation of protein domain boundaries and 3D structures for protein domains from 94 genomes (including Human, Arabidopsis, Rice, Mouse, Fly, Yeast, E. coli and Worm) has been published. Read the paper here: Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R. The proteome folding project: Proteome-scale prediction of structure and function. 2011 Aug

June 24, 2011 - Data from Keck JM, et al. (2011) added. [-Hide Details]

August 2, 2010 - Yeast Resource Center Public Image Repository (YRC PIR) launched. [-Hide Details]

The YRC PIR is a massive database of fluorescence microscopy images containing images and experimental metadata for localization, colocalization, and FRET experiments. It currently contains over 600,000 images from nearly 90,000 data files. This resource is available at http://images.yeastrc.org/. More information can be found in Riffle M, Davis TN. The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images. BMC Bioinformatics. 2010 May 19;11:263.

August 6, 2009 - Protein subcellular localization data added. [-Hide Details]

Added data formally contained in the Yeast GFP fusion localization database (Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK. Global analysis of protein localization in budding yeast. Nature. 2003 Oct 16;425(6959):671-2.) to the YRC PDR database. All of the data are now integrated into the PDR and may be viewed by searching for proteins of interest or by downloading the complete dataset at our download page.

August 5, 2008 - Launched new Philius transmembrane and signal peptide prediction server. [-Hide Details]

A new server has been launched for executing the Philius prediction algorithm on user-supplied protein sequences. The server is available at http://www.yeastrc.org/philius/.

July 14, 2008 - Protein structure data from the Human Proteome Folding (HPF) project added. [-Hide Details]

Protein domain, ab initio 3-D structure predictions and protein function predictions from the HPF added to the PDR. These data include 521,749 predicted domains for 331,671 proteins from 342 distinct organisms. More information may be found at this link.

May 8, 2008 - Added transmembrane and signal peptide predictions from Reynolds SM, et al. (2008). [+Show Details]

January 28, 2008 - Added protein complex prediction data from Qiu J, Noble WS (2008). [+Show Details]

Protein complex co-membership data has been added to the protein complex section for 2,536 proteins from Saccharomyces cerevisiae. This work is published as Qiu J, Noble WS (2008) Predicting Co-Complexed Protein Pairs from Heterogeneous Data. PLoS Comput Biol 4(4): e1000054. doi:10.1371/journal.pcbi.1000054

April 17, 2007 - Gene Ontology Term Finder Added [+Show Details]

You may now search the YRC PDR Gene Ontology mirror for specific GO terms. Terms are searched based on their accession strings, names, definitions and synonyms. Each matched term is linked to the GO Overview Page for that term, which contains a graphical interactive view of the local area of the GO graph as well as links for viewing proteins in the PDR annotated with that term. Click here to access the new GO term search form.

March 20, 2007 - Protein Complex Section and Data Added [+Show Details]

A new protein complex section has been added to the Protein Overview Page for all proteins. Protein complex data from Riffle et al. (2007, Manuscript submitted), Hazbun et al. (2003), Mewes et al. [MIPS] (2004), Krogan et al. (2006), Gavin et al. (2006), Gavin et al. (2002) and Ho et al. (2002) have been added to our database and are displayed in this section. This feature provides a simple way to see a summary of the protein complexes predicted for a particular protein for multiple studies simultaneously.

From this complex overview section, users can drill down to see highly detailed protein complex information for that protein from any of the mirrored datasets. From this detailed page, one can view even more detailed Gene Ontology analysis for each complex predicted containing this protein from the chosen study.

February 8, 2007 - Gene Ontology (GO) Term Browser Added [+Show Details]

A new GO term overview page is now incorporated into the YRC PDR. This page provides details defining the GO term, as well as a graphical representation of the GO term in the context of its position in the GO structure. All nodes displayed on this graphical representation are links to the GO overview page for the respective node, which provides a way to graphically navigate the GO graph. All GO terms presented in the PDR are linked directly to its GO term overview page. For an example, see: COMA complex.

Aug. 4, 2006 - Submit your own microscopy localization images [+Show Details]

We have added the ability for users of the YRC PDR to upload their own microscopy localization images of proteins. Once uploaded, the images will always be annotated with the reference citation provided or the name and contact information of the submitter. The uploaded data data will be fully integrated into the PDR and will be presented with all other experimental data for the protein in the database.

To upload data: First, search for and view the protein information page for which you have microscopy images. In the microscopy/localization section of that page, there is a link for uploading your own microscopy data for that protein. Following that link, you will be presented with a simple form for uploading your own data. Once submitted, the data will be reviewed by the YRC and then added to the PDR database. Each microscopy experiment you upload will have its own unique URL, and you will receive an email containing that URL when the submission is accepted. Please send any questions to Michael Riffle (mriffle@u.washington.edu).

Mar. 18, 2006 - Added new protein structure prediction data [+Show Details]

Comprehensive protein structure prediction data for Saccharomyces cerevisiae added to the PDR. 6,186 proteins were parsed into 15,809 domains using the Ginzu domain prediction algorithm. Predicted domains with no homologs were folded by ab initio using the Rosetta algorithm, and then assigned to SCOP (Structural Classification of Proteins) superfamilies. This yielded 1,432 confident structure predictions for 512 proteins. Please address correspondence relating to these data to Dr. Richard Bonneau (NYU) or Dr. Lars Malmström (Univ. of WA).

Jan. 25, 2006 - Data added for Cheeseman IM, et al. (2002) [+Show Details]

Mass spectrometry data from twelve affinity purifications added to database. This work was done in support of the following publication: Cheeseman, IM, et al. (2002). Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p. Cell 111, 163-172. For more information about these data, please contact the author(s) directly.

Jan. 25, 2006 - Data added for Widlund PO, et al. (2005) [+Show Details]

Mass spectrometry data identifying proteins from affinity purifications of BIR1 added to database. This work was done in support of the following publication: Widlund PO, et al. (2005) Phosphorylation of the Chromosomal Passenger Protein, Bir1, Is Required for Localization of Ndc10 to the Spindle during Anaphase and Full Spindle Elongation. Mol Biol Cell [Epub ahead of print] For more information about these data, please contact the author(s) directly.

Jan. 25, 2006 - New YRC PDR Launched [+Show Details]

The YRC PDR has been largely redesigned and entirely rewritten using Java, Apache Struts and Apache Tomcat. Major improvements include: more advanced searching (including GO annotations and sequence), improved protein overview page, improved data viewing pages and supporting multiple species.

The Yeast Resource Center (YRC) is a Biomedical Technology Research Center supported by the National Institute of General Medical Studies (P41 GM103533) at the US National Institutes of Health. The YRC is located in the Department of Biochemistry and Department of Genome Sciences at the University of Washington and the Department of Chemical Physiology at the Scripps Research Institute.

YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle