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The Yeast Resource Center Public Data Repository

The Yeast Resource Center Public Data Repository D378–D382 Nucleic Acids Research, 2005, Vol. 33, Database issue doi:10.1093/nar/gki073 Michael Riffle, Lars Malmstro¨m and Trisha N. Davis* Department of Biochemistry, University of Washington, Seattle, WA 98195, USA Received August 6, 2004; Revised and Accepted October 6, 2004 Perhaps the most significant aspect of the YRC PDR is that ABSTRACT it releases all of the data at a single point of access, bringing together the experimental data from many research projects (YRC PDR) serves as a single point of access for into one consolidated searchable database accessible through the experimental data produced from many collabora- the Web. Instead of going from website to website supporting tions typically studying Saccharomyces cerevisiae individual papers, one can easily search the experimental data (baker’s yeast). The experimental data include large for multiple papers at once and view the results in a single interface. As more datasets from research collaborations with amounts of mass spectrometry results from pro- the YRC become public, the database will continue to grow tein co-purification experiments, yeast two-hybrid and become an increasingly significant asset to the research interaction experiments, fluorescence microscopy community. images and protein structure predictions. All of the data are accessible via searching by gene or pro- tein name, and are available on the Web at http:// THE CONTENTS OF THE YRC PDR DATABASE www.yeastrc.org/pdr/. At the time of this writing, the YRC PDR includes data from six collaborative projects—including four publications (1–4). This includes mass spectrometry data collected through protein co-purification experiments, yeast two-hybrid protein INTRODUCTION interaction data, fluorescent microscopy images and protein The Yeast Resource Center (YRC) is an NCRR Biomedical structure prediction data. Technology Resource Center that provides expertise and Protein structures are predicted for protein domains, as otherwise costly tools of research to scientists and students parsed from the Ginzu algorithm (5). Ab initio structure pre- worldwide. This is accomplished via collaborations and tech- dictions are available as Protein Data Bank (PDB) (6) nology development projects—with 231 such collaborations formatted text, as generated using the Rosetta de novo struc- having been submitted since the beginning of 2002. The ture prediction method (7–10). collaborations focus mainly on the study of Saccharomyces In addition, the database includes images taken from silver- cerevisiae via four primary areas of expertise provided by the stained polyacrylamide gels of samples produced from protein YRC: mass spectrometry, yeast two-hybrid arrays, deconvo- co-purification experiments; and links to descriptions of the lution fluorescence microscopy and protein structure predic- protocol used for the purification. tion. The YRC investigators, who have been responsible for The breakdown of the amount of data presently included in fulfilling collaboration requests are Dr John Yates, Dr Ruedi the database is summarized in Table 1. Aebersold (mass spectrometry), Dr Stanley Fields (yeast two- hybrid), Dr Trisha Davis, Dr Eric Muller (fluorescence micro- scopy) and Dr David Baker (protein structure prediction). THE YRC PDR WEB INTERFACE Collaborative projects can involve multiple experiments carried out in one or more of these four areas. All four We have developed a simple-to-use web interface to the YRC areas can produce large amounts of data—not all of which PDR database. The primary means of interacting with the data are necessarily used in the course of publication by the col- is to perform searches based on systematic open reading frame laborator. In addition, not all collaborations necessarily lead to (ORF) or gene names. Gene names are mapped onto system- a publication; but data produced through the collaboration may atic ORF names through the publicly available Saccharomyces be valuable and useful. The YRC makes available both the Genome Database (11,12). Searching will bring the user to a published and unpublished data through the YRC Public Data page displaying an overall summary of all the experimental Repository (PDR) to the community at large. data we have for a given ORF. An example search result is *To whom correspondence should be addressed. Tel: +1 206 543 5345; Fax: +1 206 685 1792; Email: [email protected] The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact [email protected]. ª 2005, the authors Nucleic Acids Research, Vol. 33, Database issue ª Oxford University Press 2005; all rights reserved Nucleic Acids Research, 2005, Vol. 33, Database issue D379 Table 1. A summary of the quantity of the different types of data currently tagged with a fluorescent protein such as green fluorescent available in the database protein. All localization experiments involving this ORF are clearly listed here. The ‘View Images’ link provides the means Mass spectrometry data to view all images from the localization experiment, the Total runs 119 Total unique proteins identified 3138 experimental parameters used to create these images and Total peptides identified 41 397 the localization determination expressed as a cellular compo- Total gel images 45 nent term from Gene Ontology. Yeast two-hybrid data Total baits with significant hits 409 Yeast two-hybrid data Total unique ORFs with significant hits 1373 Total unique significant interactions 2031 The ORF Overview Page’s yeast two-hybrid section provides Fluorescence microscopy data the means to quickly jump to and view results from all yeast Total unique proteins localized 122 two-hybrid screens in which the ORF of interest was bait or Total full-field images 767 Total selected region images 877 prey. Screen results display the prey ORF as well as the num- Protein structure prediction ber of hits. A number of hits greater than one are considered Total ORFs with structure data 145 significant, but single hits are shown for completeness. The Total domains with structure data 255 results from these screens are also available for download as Total ab initio structures 850 (for 86 domains from 63 proteins) a tab-delimited text file. Protein structure prediction data given in Figure 1. This ‘ORF Overview Page’ is separated into If structure prediction data are available for an ORF, the pro- five sections, from which the user can view the Gene Ontology tein structure prediction section provides a list of computa- (13) description for the ORF and jump to experimental data tionally derived domains for the ORF. This section will give view pages for each of the four types of data. Each of these the start and stop residue for each domain, the source of the data view pages is tailored to a specific kind of data and each structure in the database and a link to structural information for has its own features that are described below. All data are that domain. The information in these structure links is tailored clearly labeled according to publication(s) for which they to how the structure was derived. were produced. In addition, data not used in any publication Domains, for which the structures were obtained through are clearly labeled as unpublished. ab initio prediction, will contain links to the top ten predicted structures. These structures are viewable in the site itself via Mass spectrometry data the WebMol Java applet (15). The structures are also down- From the ORF Overview Page’s mass spectrometry section, loadable as PDB text files. the user is presented with several links for viewing the mass spectrometry data. View Protocol link: This provides the user with a text AVAILABILITY description of the protocol used for a particular protein The contents of the YRC PDR are available on the Web purification, if the protocol is available. at http://www.yeastrc.org/pdr/. From this URL the contents Bait ORF link: This lists the actual purified protein and a of the database can be viewed as HTML pages, as well as link to that protein’s ORF Overview Page. Whenever the name tab-delimited text files when applicable. The entire pub- of an ORF is given in the website, it is linked to that ORF’s lished datasets of yeast two-hybrid and mass spectrometry overview page. run results are available as tab-delimited text files, linked View Gel link: If the protein sample was subjected to elec- from the front page. The unpublished datasets are available trophoresis on an SDS polyacrylamide gel, this link will be upon request. These tab-delimited text files can easily be present and will provide an image of the silver-stained gel. imported into Microsoft Excel, as well as other spreadsheet View Run link: This is a link to the results from the analysis and data software. of the protein by mass spectrometry. The data include a filtered and formatted listing produced from the DTASelect algorithm (14). The data are presented as a list of systematic ORF names FUTURE DIRECTIONS for proteins that are co-purified with the bait protein, along with its sequence coverage, number of peptides, spectrum The YRC will likely expand beyond providing collaborations count and molecular weight. A guideline for interpretation and technology development in only these four current areas of of these columns is provided on this page. For each ORF listed, expertise. As a result, the type of experimental data available there is a link for viewing the peptides that were used to make in the YRC PDR database will also expand. that identification. The list of ORFs and the peptide lists may Currently, the YRC PDR only includes experimental data be downloaded as tab-delimited text files from the site. An covering S.cerevisiae. The YRC has broadened its scope and example of the page displaying mass spectrometry data is has begun participating in collaborations involving other provided in Figure 2. organisms. As a result, the YRC PDR will contain data from protein experiments involving multiple organisms. Fluorescence microscopy (localization) data Given these two main points and the fact that the YRC PDR The ORF Overview Page’s localization section allows the user will continue to expand by the addition of data from more and to view fluorescence microscopy images of each protein more collaborations, the functionality of the interface will be D380 Nucleic Acids Research, 2005, Vol. 33, Database issue Figure 1. A screen capture of the ‘ORF Overview Page’ for the S.cerevisiae gene NSL1. This screen illustrates the result of searching for NSL1 or YPL233w. The page is separated into five distinct sections—Gene Ontology annotations, mass spectrometry, localization, yeast two-hybrid and protein structure prediction. Each section contains a summary of the experimental data relevant to NSL1 and provides links to the data. Nucleic Acids Research, 2005, Vol. 33, Database issue D381 Figure 2. A screen capture of the mass spectrometry data view page. Listed are the ORFs identified through mass spectrometry as having co-purified with the bait ORF, along with experimental data and links to peptide information. expanded to include more sophisticated searching tools, such as user in identifying more meaningful results. In addition, a searching only published data, searching by species and search- probability-based algorithm for analyzing multiple mass spec- ing by protein or gene sequence. User-controlled filters will be trometry that runs simultaneously will be added to the site, added to the mass spectrometry results in order to facilitate the allowing the user to discover probable protein complexes. D382 Nucleic Acids Research, 2005, Vol. 33, Database issue ACKNOWLEDGEMENTS 7. Bonneau,R., Tsai,J., Ruczinski,I., Chivian,D., Rohl,C., Strauss,C.E. and Baker,D. (2001) Rosetta in CASP4: progress in ab initio protein This work is supported by the National Center for Research structure prediction. Proteins, 45 (Suppl. 5), 119–126. Resources of the National Institutes of Health by a grant 8. Simons,K.T., Kooperberg,C., Huang,E. and Baker,D. (1997) Assembly of protein tertiary structures from fragments with similar local to T.N.D. entitled ‘Comprehensive Biology: Exploiting the sequences using simulated annealing and Bayesian scoring functions. Yeast Genome’, PHS No. P41 RR11823. J. Mol. Biol., 268, 209–225. 9. Simons,K.T., Bonneau,R., Ruczinski,I. and Baker,D. (1999) Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins, 37 (Suppl. 3), 171–176. 10. Simons,K.T., Ruczinski,I., Kooperberg,C., Fox,B.A., Bystroff,C. and REFERENCES Baker,D. (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent 1. Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Knight,J.R., features of proteins. Proteins, 34, 82–95. Lockshon,D., Narayan,V., Srinivasan,M., Pochart,P., Qureshi-Emili,A., 11. Dwight,S.S., Balakrishnan,R., Christie,K.R., Costanzo,M.C., Li,Y., Godwin,B., Conover,D., Kalbfleisch,T., Vijayadamodar,G., Dolinski,K., Engel,S.R., Feierbach,B., Fisk,D.G., Hirschman,J., Yang,M., Johnston,M., Fields,S. and Rothberg,J.M. (2000) Hong,E.L., Issel-Tarver,L., Nash,R.S., Sethuraman,A., Starr,B., A comprehensive analysis of protein–protein interactions in Theesfeld,C.L., Andrada,R., Binkley,G., Dong,Q., Lane,C., Saccharomyces cerevisiae. Nature, 403, 623–627. Schroeder,M., Weng,S., Botstein,D. and Cherry,J.M. (2004) 2. Drees,B.L., Sundin,B., Brazeau,E., Caviston,J.P., Chen,G.C., Guo,W., Saccharomyces Genome Database: underlying principles and Kozminski,K.G., Lau,M.W., Moskow,J.J., Tong,A., Schenkman,L.R., organisation. Brief Bioinformatics, 5, 9–22. McKenzie,A.,III, Brennwald,P., Longtine,M., Bi,E., Chan,C., Novick,P., 12. Christie,K.R., Weng,S., Balakrishnan,R., Costanzo,M.C., Dolinski,K., Boone,C., Pringle,J.R., Davis,T.N., Fields,S. and Drubin,D.G. (2001) Dwight,S.S., Engel,S.R., Feierbach,B., Fisk,D.G., Hirschman,J.E., A protein interaction map for cell polarity development. J. Cell Biol., Hong,E.L., Issel-Tarver,L., Nash,R., Sethuraman,A., Starr,B., 154, 549–571. Theesfeld,C.L., Andrada,R., Binkley,G., Dong,Q., Lane,C., 3. Hazbun,T.R., Malmstrom,L., Anderson,S., Graczyk,B.J., Schroeder,M., Botstein,D. and Cherry,J.M. (2004) Saccharomyces Fox,B., Riffle,M., Sundin,B.A., Aranda,J.D., McDonald,W.H., Genome Database (SGD) provides tools to identify and analyze Chiu,C.H., Snydsman,B.E., Bradley,P., Muller,E.G., Fields,S., sequences from Saccharomyces cerevisiae and related sequences from Baker,D., Yates,J.R.,III and Davis,T.N. (2003) Assigning function to yeast proteins by integration of technologies. Mol. Cell, 12, other organisms. Nucleic Acids Res., 32, D311–D314. 13. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., 1353–1365. 4. Sundin,B.A., Chiu,C.H., Riffle,M., Davis,T.N. and Muller,E.G. (2004) Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T., Harris,M.A., Hill,D.P., Issel-Tarver,L., Kasarskis,A., Lewis,S., Localization of proteins that are coordinately expressed with Cln2 Matese,J.C., Richardson,J.E., Ringwald,M., Rubin,G.M. and during the cell cycle. Yeast, 21, 793–800. Sherlock,G. (2000) Gene Ontology: tool for the unification of biology. 5. Chivian,D., Kim,D.E., Malmstrom,L., Bradley,P., Robertson,T., The Gene Ontology Consortium. Nature Genet., 25, 25–29. Murphy,P., Strauss,C.E., Bonneau,R., Rohl,C.A. and Baker,D. (2003) 14. Tabb,D.L., McDonald,W.H. and Yates,J.R.,III (2002) DTASelect and Automated prediction of CASP-5 structures using the Robetta server. Contrast: tools for assembling and comparing protein identifications Proteins, 53 (Suppl. 6), 524–533. from shotgun proteomics. J. Proteome Res., 1, 21–26. 6. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., 15. Walther,D. (1997) WebMol—a Java-based PDB viewer. Trends Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Biochem. Sci., 22, 274–275. Bank. Nucleic Acids Res., 28, 235–242. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Nucleic Acids Research Oxford University Press

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Publisher
Oxford University Press
Copyright
© 2005, the authors
 Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
ISSN
0305-1048
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1362-4962
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10.1093/nar/gki073
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Abstract

D378–D382 Nucleic Acids Research, 2005, Vol. 33, Database issue doi:10.1093/nar/gki073 Michael Riffle, Lars Malmstro¨m and Trisha N. Davis* Department of Biochemistry, University of Washington, Seattle, WA 98195, USA Received August 6, 2004; Revised and Accepted October 6, 2004 Perhaps the most significant aspect of the YRC PDR is that ABSTRACT it releases all of the data at a single point of access, bringing together the experimental data from many research projects (YRC PDR) serves as a single point of access for into one consolidated searchable database accessible through the experimental data produced from many collabora- the Web. Instead of going from website to website supporting tions typically studying Saccharomyces cerevisiae individual papers, one can easily search the experimental data (baker’s yeast). The experimental data include large for multiple papers at once and view the results in a single interface. As more datasets from research collaborations with amounts of mass spectrometry results from pro- the YRC become public, the database will continue to grow tein co-purification experiments, yeast two-hybrid and become an increasingly significant asset to the research interaction experiments, fluorescence microscopy community. images and protein structure predictions. All of the data are accessible via searching by gene or pro- tein name, and are available on the Web at http:// THE CONTENTS OF THE YRC PDR DATABASE www.yeastrc.org/pdr/. At the time of this writing, the YRC PDR includes data from six collaborative projects—including four publications (1–4). This includes mass spectrometry data collected through protein co-purification experiments, yeast two-hybrid protein INTRODUCTION interaction data, fluorescent microscopy images and protein The Yeast Resource Center (YRC) is an NCRR Biomedical structure prediction data. Technology Resource Center that provides expertise and Protein structures are predicted for protein domains, as otherwise costly tools of research to scientists and students parsed from the Ginzu algorithm (5). Ab initio structure pre- worldwide. This is accomplished via collaborations and tech- dictions are available as Protein Data Bank (PDB) (6) nology development projects—with 231 such collaborations formatted text, as generated using the Rosetta de novo struc- having been submitted since the beginning of 2002. The ture prediction method (7–10). collaborations focus mainly on the study of Saccharomyces In addition, the database includes images taken from silver- cerevisiae via four primary areas of expertise provided by the stained polyacrylamide gels of samples produced from protein YRC: mass spectrometry, yeast two-hybrid arrays, deconvo- co-purification experiments; and links to descriptions of the lution fluorescence microscopy and protein structure predic- protocol used for the purification. tion. The YRC investigators, who have been responsible for The breakdown of the amount of data presently included in fulfilling collaboration requests are Dr John Yates, Dr Ruedi the database is summarized in Table 1. Aebersold (mass spectrometry), Dr Stanley Fields (yeast two- hybrid), Dr Trisha Davis, Dr Eric Muller (fluorescence micro- scopy) and Dr David Baker (protein structure prediction). THE YRC PDR WEB INTERFACE Collaborative projects can involve multiple experiments carried out in one or more of these four areas. All four We have developed a simple-to-use web interface to the YRC areas can produce large amounts of data—not all of which PDR database. The primary means of interacting with the data are necessarily used in the course of publication by the col- is to perform searches based on systematic open reading frame laborator. In addition, not all collaborations necessarily lead to (ORF) or gene names. Gene names are mapped onto system- a publication; but data produced through the collaboration may atic ORF names through the publicly available Saccharomyces be valuable and useful. The YRC makes available both the Genome Database (11,12). Searching will bring the user to a published and unpublished data through the YRC Public Data page displaying an overall summary of all the experimental Repository (PDR) to the community at large. data we have for a given ORF. An example search result is *To whom correspondence should be addressed. Tel: +1 206 543 5345; Fax: +1 206 685 1792; Email: [email protected] The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact [email protected]. ª 2005, the authors Nucleic Acids Research, Vol. 33, Database issue ª Oxford University Press 2005; all rights reserved Nucleic Acids Research, 2005, Vol. 33, Database issue D379 Table 1. A summary of the quantity of the different types of data currently tagged with a fluorescent protein such as green fluorescent available in the database protein. All localization experiments involving this ORF are clearly listed here. The ‘View Images’ link provides the means Mass spectrometry data to view all images from the localization experiment, the Total runs 119 Total unique proteins identified 3138 experimental parameters used to create these images and Total peptides identified 41 397 the localization determination expressed as a cellular compo- Total gel images 45 nent term from Gene Ontology. Yeast two-hybrid data Total baits with significant hits 409 Yeast two-hybrid data Total unique ORFs with significant hits 1373 Total unique significant interactions 2031 The ORF Overview Page’s yeast two-hybrid section provides Fluorescence microscopy data the means to quickly jump to and view results from all yeast Total unique proteins localized 122 two-hybrid screens in which the ORF of interest was bait or Total full-field images 767 Total selected region images 877 prey. Screen results display the prey ORF as well as the num- Protein structure prediction ber of hits. A number of hits greater than one are considered Total ORFs with structure data 145 significant, but single hits are shown for completeness. The Total domains with structure data 255 results from these screens are also available for download as Total ab initio structures 850 (for 86 domains from 63 proteins) a tab-delimited text file. Protein structure prediction data given in Figure 1. This ‘ORF Overview Page’ is separated into If structure prediction data are available for an ORF, the pro- five sections, from which the user can view the Gene Ontology tein structure prediction section provides a list of computa- (13) description for the ORF and jump to experimental data tionally derived domains for the ORF. This section will give view pages for each of the four types of data. Each of these the start and stop residue for each domain, the source of the data view pages is tailored to a specific kind of data and each structure in the database and a link to structural information for has its own features that are described below. All data are that domain. The information in these structure links is tailored clearly labeled according to publication(s) for which they to how the structure was derived. were produced. In addition, data not used in any publication Domains, for which the structures were obtained through are clearly labeled as unpublished. ab initio prediction, will contain links to the top ten predicted structures. These structures are viewable in the site itself via Mass spectrometry data the WebMol Java applet (15). The structures are also down- From the ORF Overview Page’s mass spectrometry section, loadable as PDB text files. the user is presented with several links for viewing the mass spectrometry data. View Protocol link: This provides the user with a text AVAILABILITY description of the protocol used for a particular protein The contents of the YRC PDR are available on the Web purification, if the protocol is available. at http://www.yeastrc.org/pdr/. From this URL the contents Bait ORF link: This lists the actual purified protein and a of the database can be viewed as HTML pages, as well as link to that protein’s ORF Overview Page. Whenever the name tab-delimited text files when applicable. The entire pub- of an ORF is given in the website, it is linked to that ORF’s lished datasets of yeast two-hybrid and mass spectrometry overview page. run results are available as tab-delimited text files, linked View Gel link: If the protein sample was subjected to elec- from the front page. The unpublished datasets are available trophoresis on an SDS polyacrylamide gel, this link will be upon request. These tab-delimited text files can easily be present and will provide an image of the silver-stained gel. imported into Microsoft Excel, as well as other spreadsheet View Run link: This is a link to the results from the analysis and data software. of the protein by mass spectrometry. The data include a filtered and formatted listing produced from the DTASelect algorithm (14). The data are presented as a list of systematic ORF names FUTURE DIRECTIONS for proteins that are co-purified with the bait protein, along with its sequence coverage, number of peptides, spectrum The YRC will likely expand beyond providing collaborations count and molecular weight. A guideline for interpretation and technology development in only these four current areas of of these columns is provided on this page. For each ORF listed, expertise. As a result, the type of experimental data available there is a link for viewing the peptides that were used to make in the YRC PDR database will also expand. that identification. The list of ORFs and the peptide lists may Currently, the YRC PDR only includes experimental data be downloaded as tab-delimited text files from the site. An covering S.cerevisiae. The YRC has broadened its scope and example of the page displaying mass spectrometry data is has begun participating in collaborations involving other provided in Figure 2. organisms. As a result, the YRC PDR will contain data from protein experiments involving multiple organisms. Fluorescence microscopy (localization) data Given these two main points and the fact that the YRC PDR The ORF Overview Page’s localization section allows the user will continue to expand by the addition of data from more and to view fluorescence microscopy images of each protein more collaborations, the functionality of the interface will be D380 Nucleic Acids Research, 2005, Vol. 33, Database issue Figure 1. A screen capture of the ‘ORF Overview Page’ for the S.cerevisiae gene NSL1. This screen illustrates the result of searching for NSL1 or YPL233w. The page is separated into five distinct sections—Gene Ontology annotations, mass spectrometry, localization, yeast two-hybrid and protein structure prediction. Each section contains a summary of the experimental data relevant to NSL1 and provides links to the data. Nucleic Acids Research, 2005, Vol. 33, Database issue D381 Figure 2. A screen capture of the mass spectrometry data view page. Listed are the ORFs identified through mass spectrometry as having co-purified with the bait ORF, along with experimental data and links to peptide information. expanded to include more sophisticated searching tools, such as user in identifying more meaningful results. In addition, a searching only published data, searching by species and search- probability-based algorithm for analyzing multiple mass spec- ing by protein or gene sequence. User-controlled filters will be trometry that runs simultaneously will be added to the site, added to the mass spectrometry results in order to facilitate the allowing the user to discover probable protein complexes. D382 Nucleic Acids Research, 2005, Vol. 33, Database issue ACKNOWLEDGEMENTS 7. Bonneau,R., Tsai,J., Ruczinski,I., Chivian,D., Rohl,C., Strauss,C.E. and Baker,D. (2001) Rosetta in CASP4: progress in ab initio protein This work is supported by the National Center for Research structure prediction. Proteins, 45 (Suppl. 5), 119–126. Resources of the National Institutes of Health by a grant 8. Simons,K.T., Kooperberg,C., Huang,E. and Baker,D. (1997) Assembly of protein tertiary structures from fragments with similar local to T.N.D. entitled ‘Comprehensive Biology: Exploiting the sequences using simulated annealing and Bayesian scoring functions. Yeast Genome’, PHS No. P41 RR11823. J. Mol. Biol., 268, 209–225. 9. Simons,K.T., Bonneau,R., Ruczinski,I. and Baker,D. (1999) Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins, 37 (Suppl. 3), 171–176. 10. Simons,K.T., Ruczinski,I., Kooperberg,C., Fox,B.A., Bystroff,C. and REFERENCES Baker,D. (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent 1. Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Knight,J.R., features of proteins. Proteins, 34, 82–95. Lockshon,D., Narayan,V., Srinivasan,M., Pochart,P., Qureshi-Emili,A., 11. Dwight,S.S., Balakrishnan,R., Christie,K.R., Costanzo,M.C., Li,Y., Godwin,B., Conover,D., Kalbfleisch,T., Vijayadamodar,G., Dolinski,K., Engel,S.R., Feierbach,B., Fisk,D.G., Hirschman,J., Yang,M., Johnston,M., Fields,S. and Rothberg,J.M. (2000) Hong,E.L., Issel-Tarver,L., Nash,R.S., Sethuraman,A., Starr,B., A comprehensive analysis of protein–protein interactions in Theesfeld,C.L., Andrada,R., Binkley,G., Dong,Q., Lane,C., Saccharomyces cerevisiae. Nature, 403, 623–627. Schroeder,M., Weng,S., Botstein,D. and Cherry,J.M. (2004) 2. Drees,B.L., Sundin,B., Brazeau,E., Caviston,J.P., Chen,G.C., Guo,W., Saccharomyces Genome Database: underlying principles and Kozminski,K.G., Lau,M.W., Moskow,J.J., Tong,A., Schenkman,L.R., organisation. Brief Bioinformatics, 5, 9–22. McKenzie,A.,III, Brennwald,P., Longtine,M., Bi,E., Chan,C., Novick,P., 12. Christie,K.R., Weng,S., Balakrishnan,R., Costanzo,M.C., Dolinski,K., Boone,C., Pringle,J.R., Davis,T.N., Fields,S. and Drubin,D.G. (2001) Dwight,S.S., Engel,S.R., Feierbach,B., Fisk,D.G., Hirschman,J.E., A protein interaction map for cell polarity development. J. Cell Biol., Hong,E.L., Issel-Tarver,L., Nash,R., Sethuraman,A., Starr,B., 154, 549–571. Theesfeld,C.L., Andrada,R., Binkley,G., Dong,Q., Lane,C., 3. Hazbun,T.R., Malmstrom,L., Anderson,S., Graczyk,B.J., Schroeder,M., Botstein,D. and Cherry,J.M. (2004) Saccharomyces Fox,B., Riffle,M., Sundin,B.A., Aranda,J.D., McDonald,W.H., Genome Database (SGD) provides tools to identify and analyze Chiu,C.H., Snydsman,B.E., Bradley,P., Muller,E.G., Fields,S., sequences from Saccharomyces cerevisiae and related sequences from Baker,D., Yates,J.R.,III and Davis,T.N. (2003) Assigning function to yeast proteins by integration of technologies. Mol. 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Nucleic Acids ResearchOxford University Press

Published: Jan 1, 2005

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