Search the YRC PDR protein database:

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/.

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.

The new Philius transmembrane and signal peptide prediction algorithm was applied to 6.3 million distinct proteins in the YRC PDR database. The results for all predictions are now available on respective protein overview pages when searching for proteins. This work is described in Reynolds SM, et al. (2008) Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks. PLoS Comput Biol 4(11): e1000213. doi:10.1371/journal.pcbi.1000213.

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

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.

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.

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.

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).

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).

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.

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.

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.